Hpv detection and quantification by real-time multiplex amplification

ABSTRACT

The present invention relates to amplification primers and detection probes, which are useful for the detection of human papillomaviruses (HPV), and more particularly of HPV, which can be oncogenic for the mucosal epithelia. The amplification and detection systems provided by the present invention are group-targeted systems, namely A5-, A6- A7-, and A9-targeted systems. The amplification and detection systems of the invention allow for an amplification of HPV in multiplex as well as for a real-time detection, whereby at least the thirteen HR HPV can be detected in a single-tube assay. The invention further allows for a reliable quantitation of HPV viral loads in real-time multiplex amplification.

This application is a divisional of U.S. application Ser. No. 12/226,283 (allowed), filed Oct. 14, 2008 (published as US-2009-0275025 A1), which is a U.S. national phase of International Application No. PCT/EP2006/004314, filed 11 Apr. 2006, which designated the U.S. and the entire contents of each of which is incorporated herein by reference

FIELD

The present invention relates to the detection of human papillomaviruses (HPV), more particularly of HPV, which have a tropism for the mucosal epithelia (mucosal-type HPV), still more particularly of HPV, which can be oncogenic for the mucosal epithelia. The present invention provides amplification primers and detection probes, which are useful therefor, as well as reference template sequences suitable for designing and building such primers and probes.

BACKGROUND OF THE INVENTION

Human papillomavirus (HPV) contains a circular double-stranded DNA genome of about 7,900 bp, which is organized into three main regions, i.e.:

-   -   an early coding region containing genes E1, E2, E4, E5, E6 and         E7, which are involved in viral replication and in neoplastic         transformation,     -   a late coding region, containing genes L1 and L2, which code for         viral capside proteins,     -   a non-coding regulatory region, which is referred to as LRC         (Long Control Region), which is located between the E genes and         the L genes.

HPV constitute a group of viruses, which are associated with benign and malignant lesions of cutaneous or mucosal epithelia. To date, more than 100 different HPV types have been identified.

More than 40 HPV types belonging to the mucosal group have been detected in the anogenital mucosa.

HPV is the major risk factor in the development of squamous intraepithelial lesions (SILs), which are classified as low grade (LSIL) or high grade (HSIL) in severity.

HPV may induce cervical intraepithelial neoplasia (CIN), ranging from benign lesions (CIN1), such as condylomata acuminata, through pre-cancerous lesions (CIN2 to CIN3), up to in situ carcinoma and invasive cancer.

It is now established that HPV is directly involved in cervical carcinogenesis. Detecting HPV is essential to the prognosis of CIN and cervical cancer.

Early and precise detection of HPV is the key factor for recovery from cervical cancer.

It has also been shown that an increased HPV viral load within a cervical smear specimen is associated with an increased risk of CIN3 and of cervical carcinomas.

A number of oncogenic HPV genotypes that infect the anogenital tract have been classified as potentially high risk HPV genotypes (HR HPV), based on their occurrence or prevalence in cervical carcinomas. The presence, persistence and/or re-occurrence of HR HPV is a bad prognostic indicator. So far, thirteen HPV types are said to be HR HPV, namely HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18. Those HR HPV, which have the highest prevalence, are HPV types 33, 31, 16, 45 and 18.

Other oncogenic HPV are considered to be Low Risk HPV (LR HPV), e.g., HPV2, HPV3, HPV6, HPV11, HPV13, HPV32, HPV40, HPV42, HPV43, HPV44, HPV57.

The clinical classification of HPV types into either the HR or the LR group might evolve, or slightly diverge from one author to another, as the classification of a given HPV into the LR group only stands for as long as this HPV type is not found to be associated with a cervical carcinoma.

For example, it is now contemplated that HPV53 and HPV66 probably are HR HPV (van Ham et al. 2005, J. Clin. Microbiol. Vol. 43, n^(o)6, p. 2662-2667). Hence, the initial group of thirteen HR HPV might further increase to a number of at least 15 HPV types.

Other HPV have been described as oncogenic HPV, but without any definitive settlement on the issue of their HR or LR status, such as is the case for HPV67, HPV82, HPV85. Appropriate detection means are required to analyze their oncogenicity.

New, or yet unidentified, mucosal oncogenic HPV types may further arise. Furthermore, HPV multi-infection, involving several types of HPV, is a common situation: multi-infection is thought to account for about 20% of the HPV infection cases. An HPV multi-infection case may involve HPV types, which all are oncogenic HPV, or which comprise at least one oncogenic HPV and at least one non-oncogenic HPV. An HPV multi-infection case may involve HPV types, which all are mucosal HPV types, or may involve at least one mucosal type and at least one cutaneous type.

Also, co-infection may also occur, which involves at least one HPV and at least to one virus other than HPV, e.g., a co-infection with at least one HPV, and at least one HIV.

Such multi- and/or co-infection situations render accurate HPV detection much more difficult.

HPV primers and probes, which are suitable for the detection of mucosal oncogenic HPV, have been disclosed in prior art.

The first techniques that were developed involved type-specific probes, which were designed to detect oncogenic HPV by direct hybridization of a type-specific probe to a non-amplified HPV genome, e.g., by Southern blotting or dot blotting.

Signal-amplified tests have then been developed, such as the Hybrid Capture test (HC2®) of Digene Corporation, Gaithersburg, Md., USA. The HC2® test has been approved by the FDA, and is at present time the reference test for clinical diagnosis.

The HC2® system is a liquid phase microplate system using DNA/RNA hybridization assay, which does not comprise any target amplification: viral DNA hybridizes in liquid phase to a RNA probe which targets the 13 HR HPV, the hybrids thus formed being detected by anti-DNA/RNA antibodies and visualized by chemoluminescence.

The HC2® test is a sensitive assay. It however is only of qualitative value. Viral loads assessed by the HC2® test does not increase with increasing grade of SIL, and are not sufficiently reliable in case of multiple HPV infections. Hence, the HC2® test is not a quantitative assay.

As the HC2® test does not reflect the viral load initially contained in the analyzed sample, it is recommended to combine it with classic cytology, to distinguish the cases with high grade lesions from those without high grade lesions.

Amplification methods have then been developed, wherein HPV target(s) is(are) amplified by at least one primer pair, the amplicon thus produced being detected either by this (labelled) primer pair or by a probe.

Such prior art primers have first been designed as general consensus primers, which are intended for amplifying several HPV, usually several of the thirteen HR HPV, as well as other HPV (oncogenic LR, and sometimes also non-oncogenic HPV).

Such consensus primers are also referred to as “universal” primers. These consensus primers target conserved regions in the HPV L1 gene (e.g., the is MY09/MY11/HMB01 primers, the GP5+/GP6+ primers, the PGMY09/PGMY11 primers, and the SPF1/SPF2 or SPF10 primers), or the E1 ORF region (e.g., the CPIIG/CPI primers described in Tieben et al. 1993, J. Virol. Methods 42:265-279).

To render consensus PCR applicable to clinical diagnosis, HPV probes have been developed to detect and type HPV amplicons generated by consensus primer sets. Detection of the HPV amplicons generated by consensus primers is usually performed by a reverse hybridization line blot assay, or by colorimetric microtiter plate-based enzyme immunoassay.

Illustrative of such consensus PCR methods are the INNO-LiPA HPV test (Innogenetics, Gent, Belgium), and the Amplicor HPV test (Roche Molecular Systems, Branchburg, N.J., USA).

The INNO-LiPA HPV test is a reverse hybridization line probe assay, the prototype research version of which has been described in Kleter et al., 1999 (Journal of Clinical Microbiology, vol. 37, n^(o)8, p. 2508-2517), and Kleter et al. 1998 (American Journal of Pathology, vol. 153, n^(o)6, p. 1731-1739),

Briefly, a PCR primer set is used to generate a short PCR fragment (SPF PCR) of 65-bp from the L1 open reading frame. The prototype research INNO-LiPA primer set consists of 10 biotinylated primers (referred to as the SPF10 primer set), namely the six primers of the SPF1/2 system (described in Kleter et al. 1998), and four additional primers (MY09/11 and GP5+/6+).

The SPF10 amplimers are denatured, and incubated under hybridization conditions with poly(dT)-tailed type-specific oligonucleotide probes, which are immobilized as parallel lines on nitrocellulose membrane strips. The probe strips are then washed out for detection of the retained hybrids.

The INNO-LiPA HPV test allows the detection of at least 25 HPV genotypes (the 13 HR HPV, i.e., HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45, 18, as well as other HPV, e.g., HPV 6, 11, 34, 40, 42, 43, 44, 53, 66, 70, and 74). It is a genotyping line probe assay, and is of qualitative value. The INNO-LiPA HPV test is not a quantitative assay.

The Amplicor HPV test uses amplification of target HPV DNA by PCR followed by is nucleic acid hybridization for the detection of the thirteen HR HPV. The Amplicor HPV test amplifies a sequence of about 165 bp within the L1 region. The primer sets consist of 12 primers, which have been designed as general consensus primers, to amplify the initial group of 13 HR HPV. After amplification and denaturation, the amplified HPV sequences are distributed in a microwell plate, and incubated with L1 capture probes, the hybrids being detected and visualized by colorimetric enzyme immunoassay (avidin-horseradish peroxidase conjugate). The Amplicor HPV test has been reported as being of higher analytical specificity, compared to the HC2® test (less false negative results; see Poljak et al. 2005, Acta Dermatoven APA, vol. 14, n^(o)4, p. 147-152).

The Amplicor HPV test is sensitive, but its HPV spectrum is restricted to those 13 HPV, which have been initially considered as being the HR HPV. For example, the Amplicor HPV test does not detect HPV66 and HPV53, which are now thought to be HR HPV. In other words, the Amplicor test is not designed to be adaptive to any change or evolution in HPV classification or knowledge.

Furthermore, the Amplicor HPV test is not a quantitative assay.

These line blot or microwell-based prior art techniques use consensus HPV primers, i.e., primers which result from sequence alignment of a pre-determined set of selected oncogenic HPV, and from the determination of those consensus sequences, which have a sufficient similarity or identity score with all of the selected HPV, to hybridize to all of them. Consensus primers are thus designed to amplify a predetermined sub-set of oncogenic HPV, and may not succeed in amplifying other oncogenic HPV (such as HR new corners, or non-HR oncogenic HPV).

Such a consensus approach is restricted by the possibility of determining primer sequences, which would still sufficiently hybridize to the ever increasing and ever evolving desired targets.

If one or several new oncogenic HPV strain(s) appear, such prior art consensus primers might give false negative results.

Also, none of the prior art line blot or microwell-based techniques is of a quantitative nature, whereas recent findings show that the HPV copy number accounts for the phase and/or severity of the disease, and/or have a diagnostic and/or prognostic value in the field of oncogeny.

Absence of quantitative performance limits the spectrum of clinical applicability, as such tests cannot give information on the actual cancer risk level, or on the actual cancer grade.

Moreover, according to these prior art consensus line blot or microwell-based techniques, the detection step is an additional and tedious step, which has to be performed as a separated step after amplification has occurred.

Real-time PCR amplification techniques have recently been developed for the detection of HPV16 or HPV18 (Hesselink et al. 2005, Journal of Clinical Microbiology, vol. 43, n^(o)9, p. 4868-4871; Gravitt et al. 2003, Cancer Epidemiology, Biomarkers & Prevention, vol. 12, p. 477-484).

These real-time PCR either are based on FRET (LightCycler), or use TaqMan probes (Applied Biosystems).

Compared to prior art line blot or microwell-based techniques, such real-time PCR have the advantage of combining amplification and detection in one single step, and of opening the way to quantification.

For example, van Duin et al. 2002 (Int. J. Cancer, vol. 98, n^(o)4, p. 590-595) describes a quantitative real-time PCR assay for the detection of HPV16.

Prior art real-time PCR protocols however are type-specific PCR protocols, which are limited to the detection of only one HPV per amplification run, and more particularly to the sole detection of HPV16 or HPV18. They thus represent valuable research tool, but have a very limited clinical applicability.

Attempts have been made to develop multiplex real-time PCR amplification of HPV. These attempts are however limited to duplex or triplex real-time PCR for the detection of HPV16, HPV18, HPV45. For example, Szuhai et al. 2001 (American Journal of Pathology, 159(5): 1651-1660) disclose seven type-specific molecular beacons, which are said to be type-specific molecular beacons, namely five HR HPV molecular beacons (HPV16, 18, 31, 33, 45) and two LR HPV molecular beacons (HPV6, 11); see table 1 of Szuhai et al. These molecular beacons are described as being useful for the detection of amplicons generated by the CPI/CPIIG “universal” primers. Multiplex attempts are disclosed in Szuhai is et al., but are limited to duplex or triplex assays (HPV16, HPV18, HPV45). The authors explicitly indicate that “although the multiplexing capacity of molecular beacon PCR is higher than three, it is unlikely that it will approach the number of different HPV genotypes” (see page 1656, right-hand column, second paragraph). For this reason, the authors came to the conclusion that type-specific molecular beacons cannot by their own solve the problem of HPV clinical diagnosis, and that they shall be used in combination with a general pre-screening HPV detection method, to arrive at a two-step HPV detection and genotyping strategy (see e.g., FIG. 6 of Szuhai et al.), wherein type-specific HPV molecular beacon PCR is disclosed to be used in combination with a SybrGreen general primer PCR pre-screening.

Hence, to the best of the inventors' knowledge, prior art does neither describe nor suggest any real-time amplification technique that could be worked in multiplex, whilst retaining the required HPV detection specificity, which would allow to cover at least the 13 HR HPV in a single step (amplification+detection) run. Furthermore, to the best of the inventors' knowledge, prior art does not describe any quantitative real-time HPV amplification technique, which would allow to cover at least the five most common HR HPV (namely, HPV16, 18, 45, 31 and 33), preferably at least the 13 HR HPV, more preferably at least the 13 HR HPV as well as five other oncogenic HPV, in a single step (amplification+detection) run, and which would be quantitative, even when implemented in multiplex.

ABSTRACT OF THE INVENTION

The present invention relates to the detection of HPV by amplification, more particularly of mucosal-type HPV, still more particularly of HPV, which can be oncogenic for the mucosal epithelia.

The present invention allows the detection of at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV (HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45, 18), most preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85).

The present invention relates to amplification primer systems, and to detection probe systems, as well as to the amplification-detection systems (i.e. real-time amplification systems), which result from the combination of at least one amplification primer system of the invention and at least one detection probe system of the invention.

The present invention also relates to reference template HPV sequences, which are suitable for the production of amplification primers and detection probes of the invention, as well as to amplicons obtainable by amplification of an HPV nucleic acid with at least one amplification primer system of the invention, and optionally by detection with at least one detection probe system of the invention.

The present invention further relates to the biological and pharmaceutical applications thereof, more particularly to the diagnostic and prognostic applications thereof, notably in the field of CIN and cervical cancer.

The HPV amplification method of the invention is based on an approach of HPV tropism and oncogenicity, which is completely different from, and completely innovative compared to prior art approaches: contrary to the global consensus approaches, or to the type-specific approaches, which prior art methods have up to now followed, the present inventors have designed and built an approach, which is an HPV group-based approach (see the phylogenetic tree shown in FIG. 1, which has been built by the present inventors). According to the inventors' HPV group-based approach, amplification primer systems and detection probe systems are provided for each HPV group that comprises at least one HPV type capable of being oncogenic for the mucosal epithelia, namely at least for each of groups A6, A5, A9 and A7.

Indeed, the present inventors have selected appropriate targets within each of said HPV groups, which are suitable for the production of primers and probes covering

at least the five most common HR HPV (namely, HPV16, 18, 45, 31 and 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV is belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85), in a single step (amplification+detection) run.

The selected targets of the present invention are reference template sequences, which allow designing and building primers (hybridizing to one end of said selected targets, or to the complementary sequence thereof), as well as amplicon-annealing probes, which allow to cover said HPV in a single step (amplification+detection) run.

The amplification primer systems of the present invention are targeted to the HPV of group A6 or A5 or A9 or A7, and are intended to amplify as many HPV types belonging to one of these groups as possible.

The detection probe systems of the present invention allow the detection of one or several of the amplicon(s) obtainable by amplification of a given HPV by an amplification system of the present invention. They are targeted to group(s) A6 and/or A5 and/or A9 and/or A7, and are especially adapted to implementation in real-time with said amplification primer systems.

The detection probe systems of the invention comprise probes, which allow for the general detection of at least one HPV that belongs to the HPV set formed by groups A6 and A5 and A9 and A7, as well as more precise detections, such as:

-   -   the detection of at least one HPV that belongs to group A6 or A5         or A9 or A7, or     -   the detection of at least one HPV that belongs to a sub-set of         group A6 HPV, or of group A5 HPV, or of group A9 HPV, or of         group A7 HPV, or     -   the detection of at least one particular HPV type.

The present invention thereby provides a great flexibility of precision levels for the detection of HPV. Such flexibility has, to the best of the inventors' knowledge, never has been previously attained.

The present invention further provides A6- and/or A5- and/or A9- and/or A7-targeted systems, resulting from the combination of at least one amplification primer system of the invention and at least one detection probe system of the invention.

The present invention more particularly provides A6- or A5- or A9- or A7-targeted systems, which comprise at least one amplification primer system of the invention and at least one detection probe system of the invention, wherein said at least one amplification primer system and said at least one detection probe system are targeted to the same group, i.e., A6 or A5 or A9 or A7.

Most of the amplification primer and/or detection probe systems of the present invention comprise more than two primers and/or more than one probe. Hence, most of the amplification primer and/or detection probe systems of the invention, and notably the A9-targeted systems, and the A7-targeted systems, already are by themselves multiplex systems.

According to a very advantageous feature of the present invention, the group-targeted systems of the present invention are suitable for use together in a single-tube amplification, i.e., the present invention allows for implementation of at least one A6-targeted system, and at least one A5-targeted system, and at least one A9-targeted system, and at least one A7-targeted system, together in a single-tube assay, thereby resulting in what could be called a multi-multiplex, i.e., a “megaplex” amplification and/or detection: see e.g., in the examples below, illustrative “megaplex” involving 17 primers and 12 probes, which are capable of amplifying and detecting seventeen oncogenic mucosal-type HPV in a single-tube assay, without any significant loss in specificity, and without any significant loss in sensitivity.

Hence, the amplification primer systems and detection probe systems are specifically adapted to real-time multiplex amplification.

To the best of the inventors' knowledge, there is no prior art method, which would allow for a real-time multiplex amplification of at least the five most common HR HPV, preferably at least 7 HR HPV, still preferably the five most common HR HPV to as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV.

Advantageously, the present invention allows for the detection of at least 18 oncogenic mucosal-type HPV in a single-tube assay, namely the 13 HR HPV, as well as five other oncogenic HPV (HPV66, 53, 82, 67, 85).

A further advantageous aspect of the present invention is that it is especially adapted to HPV viral load quantification. The HPV method of the invention is able to remain specific and quantitative, even when implemented in a single-tube multiplex.

The amplification primer systems and detection probe systems are specifically adapted to real-time quantitative multiplex amplification, and retain this capacity even when implemented in a “megaplex” mode comprising at least one A6-targeted system, and at least one A5-targeted system, and at least one A9-targeted system, and at least one A7-targeted system, together in a single-tube assay.

To the best of the inventors' knowledge, there is no prior art method, which would allow for a real-time quantitative multiplex amplification of said at least five most common HR HPV, preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, more preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85).

The amplification primer systems and the detection probe systems of the invention all share the special technical feature of being designed and built according to a group-based approach of HPV oncogenicity, and of being suitable for implementation together in a the same assay tube.

More particularly, they enable a real-time “megaplex” implementation covering at least the five most common HR HPV types, preferably at least 7 HR HPV (e.g., HPV 56, 51, 33, 31, 16, 45, 18), still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, more preferably at least 18 oncogenic mucosal-type HPV (i.e., at least the 13 HR HPV, and five other oncogenic HPV, e.g., HPV66, 53, 82, 67, 85), in a single-tube assay, without any significant loss in the qualitative accuracy of the HPV detection.

The amplification primer systems and the detection probe systems of the invention further show levels of specificity, Ct and sensitivity, which are sufficiently homogeneous to allow for a real-time “megaplex” amplification, which is of quantitative value.

The group-based approach of the present invention further provides flexibility to the amplification and/or detection systems, as their intrinsic design is likely to make them suitable for detection of any oncogenic HPV “new corner” that may arise by mutagenesis.

The group-based approach of the present invention also confers flexibility in the use for clinical diagnosis: depending on the choice of probe system(s) that is made by the user, the precision level in HPV detection can range from a general response indicating the detection of at least one HPV belonging to the set formed by groups A6 and A5 and A9 and A7, to the very precise response indicating the detection of at least one particular HPV type. To the best of the inventors' knowledge, such flexibility has up to now never been attained.

The group-based approach of the present invention further is suitable for providing accuracy in case of multi- and/or co-infections.

It is believed that such an achievement represents a technological breakthrough, compared to prior art HPV detection systems.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: phylogenic tree of the present invention;

FIGS. 2A and 2B: schematic presentation of the amplification targets for HPV groups A6 (HPV56) and A5 (HPV51) (FIG. 2A), and for groups A9 (HPV16) and A7 (HPV18) (FIG. 2B);

FIG. 3: reprint of NCBI_(—)001594.1, sequence of HPV56 (reference HPV for group A6); SEQ ID NO:420;

FIG. 4: reprint of NCBI_(—)001533.1, sequence of HPV51 (reference HPV for group A5); SEQ ID NO:421;

FIG. 5: reprint of NCBI_(—)001526.1, sequence of HPV16 (reference HPV for group A9); SEQ ID NO:422;

FIG. 6: reprint of NCBI_(—)001357.1, sequence of HPV18 (reference HPV for group A7); SEQ ID NO:423;

FIG. 7: convention for positions, which is followed in present application.

All sequences, including reverse primers, are listed in their 5′ to 3′ orientation. Start and stop positions on a reference HPV sequences are given in increasing value order. Hence:

-   -   concerning primers: start and stop positions are either the         start and stop positions of the reference HPV fragment, to which         the sequence of the primer corresponds (case of forward primer),         or the start and stop positions of the reference HPV target         fragment, to which the primer anneals (case of the reverse         primers);     -   with regards to the probes: as a probe and its complementary         sequence are, at least in simplex amplification, products, which         have equivalent functions, the start and stop positions are         either those of the reference HPV fragment, to which the         sequence of the probe corresponds, or those of the reference HPV         target fragment, to which the probe anneals.

DETAILED DESCRIPTION

The present invention is based on an approach, which is completely different from, and truly innovative, compared to prior art techniques. The invention overcomes the drawbacks of prior art techniques, and has numerous advantages, notably in terms of clinical applicability, performance, reliance and flexibility.

As mentioned in the above “background” section, prior art primers are designed either as type-specific primers, or as general consensus primers by classic alignment of as many mucosal HPV sequence as required, or desired, or as possible (e.g., by direct alignment of the 13 HR HPV).

On the contrary, the primers of the invention have been designed by HPV groups (=HPV genera).

Indeed, the present inventors analyzed the phylogeny of HPV, and have constructed the resulting phylogenic tree, which is shown in FIG. 1.

The present inventors selected one HPV sub-family, which is involved in carcinogenesis of the mucosal epithelia, namely sub-family A. They further selected a set of HPV types, which is representative of HPV sub-family A. This representative set consists in 35 different HPV types, among which 18 types are mucosal HPV, which are at least potentially oncogenic HPV (i.e., the 13 HPV known as the 13 HR; two potentially HR HPV -HPV53 and HPV66-; and three other HPV, which are believed to have an oncogenic potential -HPV82, HPV67 and HPV85-), the remaining 17 other HPV types being up to now known as being non-oncogenic HPV (see FIG. 1).

The inventors thus came to the conclusion that those HPV, which have a tropism for the mucosal epithelia, and which are at least potentially oncogenic HPV, are distributed among groups A6, A5, A9 and A7 (see FIG. 1). More precisely, said mucosal oncogenic HPV are distributed among:

-   -   group A6, for HPV66, HPV56, HPV53;     -   group A5, for HPV51, HPV82;     -   group A9, for HPV58, HPV33, HPV67, HPV52, HPV35, HPV31, HPV16;     -   group A7, for HPV68, HPV39, HPV85, HPV59, HPV45, HPV18.

By “HPV, which is at least potentially oncogenic”, it is meant that said HPV is either known to be oncogenic (such as those 13 HPV, which are usually referred to as the 13 HR HPV, as well as other oncogenic HPV, such as HPV66, HPV53, and HPV82), or which have been described at least by some authors as potentially oncogenic (such as HPV85), or which would be in the future described as associated to a tumorous mucosa.

The design by group is a special feature shared by all the products of the invention.

In addition to covering at least the five most common HR HPV types, preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the thirteen HR HPV types, in a single-tube experiment, the means offered by the present invention is likely to detect any particular variant that a patient may have. Hence, the method of the invention is much safer than any prior art method.

In case of multiple HPV infections, several HPV types are present in the collected sample. A competitive effect may then be observed, wherein one HPV type takes prevalence over another one for the same consensus primer. Detection of the competed HPV may then be hampered, although the primer has initially been designed to hybridize to both HPV.

The present invention further has the advantage of enabling the analysis of multi- and/or co-infection cases, without any loss in specificity and sensitivity.

The present invention thus relates to amplification primer systems, to detection probes system, and to pharmaceutical compositions, biological compositions, and detection kits comprising at least one of said amplification and detection systems. The present invention also relates to a method of HPV detection, which comprises the amplification of at least one HPV nucleic acid fragment, by at least one amplification primer system of the invention, and which optionally comprises the detection of the amplicon(s) thereby produced, by at least one detection probe system of the invention.

The HPV detection method of the invention is notably useful for the diagnosis of an HPV-related disease or condition, for the prognosis or risk assessment of such an HPV-related disease or condition, for monitoring of the evolution of an HPV-related disease or condition, for monitoring the efficiency of an anti-HPV drug or treatment, such as e.g., an anti-HPV vaccine or an anti-HPV vaccine candidate (e.g., an anti-HPV16 and/or anti-HPV18 and/or anti-HPV45 vaccine, or vaccine candidate).

Said HPV-related disease or condition is any disease or condition involving HPV, and more particularly an HPV-related neoplasia (e.g., cervical intraepithelial neoplasia) or cancer, such as a cervical cancer.

The present invention thus provides amplification primer systems and detection probe systems, which are targeted to the oncogenic HPV of group A6, and/or to the oncogenic HPV of A5, and/or to the oncogenic HPV of A9, and/or to the oncogenic HPV of A7.

Most of the amplification and/or detection systems of the present invention are multiplex systems, which comprises more than two primers and/or more than one probe. It is notably the case of the A9-targeted systems and of the A7-targeted systems.

Each amplification primer system can be implemented with an amplification primer system of another group in a single-tube amplification assay, without any significant loss in specificity. Hence, at least one A6-targeted amplification primer system of the present invention and at least one A5-targeted amplification primer system of the present invention and at least one A9-targeted amplification primer system of the present invention and at least one A7-targeted amplification primer system of the present invention, can be used together in a single-tube amplification assay, without any significant loss in specificity.

For each amplification primer system, the invention provides at least one detection probe system, thereby forming an amplification and detection system (i.e., a real-time amplification system).

Each detection probe system of the present invention can be implemented with its corresponding amplification primer system in a single-tube assay, without any significant loss in specificity, thereby allowing for a real-time HPV amplification and detection.

The present invention thus provides with group-targeted amplification and detection systems, namely:

-   -   several A6-targeted amplification and detection systems,     -   several A5-targeted amplification and detection systems,     -   several A9-targeted amplification and detection systems,     -   several A7-targeted amplification and detection systems.

Each amplification and detection system can be implemented with an amplification and detection system of another group in a single-tube amplification assay, without any significant loss in specificity, thereby allowing for a single-tube multi-multiplex (or “megaplex”) real-time amplification and detection of those HPV, which have a tropism for the mucosal epithelia, and which are at least potentially oncogenic HPV.

Hence, at least one A6-targeted amplification and detection system of the present invention, and at least one A5-targeted amplification and detection system of the present invention, and at least one A9-targeted amplification and detection system of the present invention, and at least one A7-targeted amplification and detection system of the present invention, can be used together in a single-tube amplification assay, without any significant loss in specificity.

Whilst the invention provides systems, which are especially adapted to multiplex or multi-multiplex implementation, the implementation of a system of the invention in simplex mode is of course also encompassed by the present invention.

The amplification and detection systems of the present invention further have levels of Ct and sensitivity, which are sufficiently homogeneous to allow for a quantitative HPV amplification and detection. The present invention thereby allows for the identification of the presence of one or several mucosal HPV in a single-tube assay, as well as for the determination of the viral HPV load(s). The quantitative property of the present invention is retained, even when it is implemented in a “megaplex” mode.

The invention thus relates to group-targeted amplification and/or detection systems, and to their use for the detection of mucosal HPV, said group-targeted amplification and/or detection systems sharing the special technical feature of being suitable for multiplex (in fact, multi-multiplex, i.e., “megaplex”) amplification and for real-time detection thereof, whereby these systems allow for the detection in a single-tube assay of at least the five most common HR HPV (i.e., HPV16, 18, to 45, 31, 33),

preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18), more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53 still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53 even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53 most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85, still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53.

The group-targeted amplification and/or detection systems of the present invention further share the special technical feature of allowing such a real-time “megaplex” amplification to be quantitative.

As above-mentioned, the amplification and detection systems of the present invention are based on a truly innovative group-based approach.

Indeed, according to prior art general consensus techniques, the design of the primers (also referred to as “universal” primers) is made by alignment of all HPV sequences to be amplified, e.g., the 13 HR HPV, and determination of consensus sequences, which targets as many of the 13 HPV as possible. Hence, such consensus sequences are found in a conserved gene or region, such as a gene of late coding region (e.g., gene L1), and the same conserved gene or region is selected for the whole set of HPV to be amplified.

On the contrary, the present inventors made a design per HPV group, i.e., they selected appropriate targets for each HPV group. More particularly, they selected genes of the early coding region, more particularly genes E1, E2, E6, E7. The present inventors have designed particular targets for each the desired HPV groups.

For example, the primers, which have been designed for group A5, have their target within genes E7, E1; the primers, which have been designed for group A6, have their target within genes E6, E7; the primers, which have been designed for group A7, have their target within gene E1; and the primers, which have been designed for group A9, have their target within genes E1, E2. Illustrative targets of the invention are shown in FIGS. 2A (groups A5 and A6) and 2B (groups A7 and A9).

Hence, the present inventors selected reference template sequences for each of groups A5, A6, A7 and A9, wherein the A5 reference template sequences are within the region consisting of genes E7 and E1, the A6 reference template sequences are within the region consisting of genes E6 and E7, the A7 reference template sequences are within gene E1, and the A9 reference template sequences are within the region consisting of genes E1 and E2.

The primers are designed and built to hybridize to one end of said targets (or to the complementary sequence thereof), whereby a primer pair anneals to each end of said target (or to the complementary sequence thereof).

The probes are designed and built to anneal to one of said reference template sequences, whereby each probe anneals to at least one of the amplicons generated by a primer system of the invention.

An amplification primer system of the invention comprises at least two primers. A detection probe system of the invention comprises at least one probe.

The amplification primer systems of the invention preferentially amplify HPV that belong to group A6 or A5 or A9 or A7, i.e., oncogenic HPV.

The present inventors further succeeded in producing amplification primer systems, which are specific of the HPV set formed by groups A5 and A6 and A7 and A9. These amplification primer systems of the invention do not amplify any HPV that would belong to a group other than A5, A6, A7, A9. Indeed, most primer systems of the invention are specific of the HPV set formed by groups A6 and A5 and A9 and A7.

Moreover, most of amplification primer systems of the invention are specific of the group to which they are targeted, i.e., most primer systems of the invention are specific of group A6 or A5 or A9 or A7: most primers of a given amplification system amplify one or several HPV of the same HPV group, without amplifying is any HPV that would belong to another HPV group.

Those primer systems of the invention, which are not specific of the HPV set formed by groups A5 and A6 and A7 and A9, may amplify nucleic acids that are not from an HPV of said groups, e.g., a non-oncogenic HPV. In such a case, these primer systems of the invention do however show a much lower amplification efficiency for these non-target amplicons (e.g., they lead to a PCR efficiency that is much lower than the one obtained for HPV of groups A5 and/or A6 and/or A9 and/or A7, and are therefore not quantitative).

When a group-targeted primer system of the invention is combined with a probe system of the invention that is targeted to the same group, the group-targeted real-time amplification system that results therefrom is specific of the HPV set formed by groups A5 and A6 and A9 and A7: none of such real-time amplification systems detects an HPV that would not belong to group A5 or A6 or A9 or A7. Furthermore, most of these real-time amplification systems are specific of the group to which they targeted.

Only one real-time amplification system of the invention has a cross-group reactivity: the real-time amplification primer system designed for group A9, which is referred to in the examples below as system C, detects the seven HPV types of group A9, and also HPV53, which is an oncogenic HPV belonging to group A6 (HPV53 being a potentially HR HPV); this group A9 system C does however not detect any other HPV among the 42 HPV tested (no group A6 HPV other than HPV53; no group A5 HPV; no group A11 HPV; no group A7 HPV, no group A4 HPV; no group A3 HPV).

In any case, does a real-time amplification system of the present invention detect a nucleic acid that would be a human nucleic acid.

When it is desired to amplify any HPV, which belongs to group A6, A5, A9, or A7, most of the amplification primer systems of the present invention will in fact comprise more than two primers, i.e., at least three primers.

For example, the amplification primer systems, which are targeted to group A6 or A5, only require a primer pair to amplify HPV56 and optionally HPV66 (for group A6), or HPV51 and optionally HPV82 (for group A5). But, those amplification primer systems, which are targeted to group A9 or A7, have to amplify six or seven HPV types of group A9, or five or six HPV types of group A7, if a complete coverage of the HPV spectrum of the group is desired. Under such instances, an A9- or A7-targeted amplification system of the invention may comprise e.g., at least three or four forward primers, and two, three, four, five or more reverse primers. Such A9- or A7-targeted amplification primer systems therefore are already multiplex systems by themselves.

Of course, the skilled person, who would like to restrict the spectrum of amplified HPV, might select fewer forward and/or reverse primers, depending on which HPV types or strain he/she would like to amplify.

Similarly, when it is desired to detect any HPV, which belongs to group A6, A5, A9, or A7, most of the detection probe systems of the present invention will in fact comprise more than one probe, i.e. at least two probes.

For example, the detection probe systems, which are targeted to group A6 or A5, only require probe to detect HPV56 and optionally HPV66 (for group A6), or HPV51 and optionally HPV82 (for group A5). But, those detection probe systems, which are targeted to group A9 or A7, may comprise one probe per HPV type or strain to be detected, notably when a both a complete coverage of the HPV group spectrum, and a simultaneous HPV group or type discrimination are desired. An A9- or A7-targeted detection probe system may thus comprise at least four probes, for example four, five or six probes.

As above-mentioned, all detection probe systems of the present invention are adapted to real-time detection, and can thus be implemented with their corresponding amplification primer systems in the very same tube.

In the examples below, are described several A6-, A5-, A9 and A7-targeted amplification and/or detection systems of the invention.

In these examples, are shown table 12 to table 88:

-   -   tables 12-35: these tables gives the SEQ ID NO: and positions of         the reference amplicons (the sequences of these reference         template amplicons are also listed after the last table, i.e.,         before the “claims” section), the forward primers, the reverse         primers, the probes, the beacons probes of illustrative         group-targeted systems of the invention;     -   tables 35-50: these tables show the number of nucleotide         mismatches shown by primers and probes of the invention         (alignment of the sequences of 50 HPV types); an empty box         indicates there is no coherent sequence alignment;     -   tables 51-68: specificity of the detection systems of the         invention;     -   tables 69-82: system sensitivity;     -   tables 83-88: “megaplex” specificity and sensitivity,     -   table 89: list of HPV genome sequences.

A reference genome has been elected for each HPV group, namely:

-   -   for group A5: the reference genome is the genome sequence of         HPV51 available under accession number NC_(—)001533.1,     -   for group A6: the reference genome is the genome sequence of         HPV56 available under accession number NC_(—)001594.1,     -   for group A7: the reference genome is the genome sequence of         HPV18 available under accession number NC_(—)001357.1,     -   for group A9: the reference genome is the genome sequence of         HPV16 available under accession number NC_(—)001526.1,

In the following tables, the term <<address>> means a nucleotide position in the reference genome. More precisely:

-   -   a forward primer having an address X is an isolated         oligonucleotide, which has a sequence which is the sequence of a         fragment of the reference genome starting at position X in said         reference genome, or a variant of such a fragment sequence (see         the mismatch count tables below),     -   a reverse primer having an address X is an isolated         oligonucleotide, which has a sequence which is complementary to         the sequence of a fragment of the reference genome ending at         position X in said reference genome, or a variant of such a         fragment sequence (see the mismatch count tables below),     -   a probe having an address X is an isolated oligonucleotide, the         sequence of which is the sequence of a fragment of the reference         genome starting at position X in said reference genome, or which         is the complementary sequence of such a fragment sequence (over         the entire length of this fragment sequence), or a variant of         such a fragment sequence or of such a complementary fragment         sequence (see the mismatch count tables below).

As a consequence, when a primer pair, which is selected from a given system, to consist of a forward primer having the address Xf, and of a reverse primer having the address Kr, is implemented on its reference HPV genome under conditions favorable to nucleic acid amplification, this primer pair then amplifies from said HPV reference genome an amplicon, which consists of the sequence that extends from position Xf to position Xr in said reference HPV genome (start and stop positions included).

When this primer pair is, under conditions favorable to nucleic acid amplification, implemented on a given HPV genome, which is not its reference HPV genome, but which belongs to the same group as this reference HPV genome, this primer pair then amplifies from said given HPV genome an amplicon, which consists in the sequence of the fragment of said given HPV genome, which corresponds by sequence alignment to the fragment that extends from position Xf to position Xr in said reference HPV genome.

A fragment A, which is a fragment of a given HPV genome and, which corresponds by sequence alignment to a fragment B of a HPV reference genome, means that said fragment A has the same length as said fragment B, and that the start and stop positions of said fragment A within said given HPV genome are such that, among those fragments of said given HPV genome, which have the same length as said fragment B, said fragment A is the fragment, which gives the best identity score when compared to the nucleotide sequence of said fragment B, as determined by global alignment to the nucleotide sequence of fragment B.

It will also be understood that:

-   -   a forward primer having an address Xf and a length Lf is an to         isolated oligonucleotide, which has a sequence which is the         sequence of a fragment of the reference genome starting at         position Xf in said reference genome, and ending at position         Xf+Lf-1 in said reference genome, or a variant of such a         fragment sequence (see the alignments shown below),     -   a reverse primer having an address Xr and a length Lr is an         isolated oligonucleotide, which has a sequence which is         complementary to the sequence of a fragment of the reference         genome starting at position Xr−Lr−1, and ending at position Xr         in said reference genome, or a variant of such a fragment         sequence (see the alignments shown below),     -   a probe having an address Xp and a length Lp is an isolated         oligonucleotide, the sequence of which is the sequence of a         fragment of the reference genome starting at position Xp and         ending at position Xp+Lp−1 in said reference genome, or which is         complementary to such a fragment sequence, or a variant of such         a fragment sequence or of such a complementary fragment sequence         (see the alignments shown below).

The present invention thus relates to a process for the nucleic acid amplification of at least one HPV target, wherein said HPV is an HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV target, most preferably at least one oncogenic cervical HPV. The amplification process of the invention comprises the step of producing from said at least one HPV target at least one amplicon by means of at least two primers.

According to an advantageous embodiment of the present invention, the amplification process of the present invention can be a real-time multiplex amplification process, involving at least one probe that can anneal to the amplicon(s) generated by said t least two primers.

The present invention relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample. The detection process of the present invention comprises the detection of at least one nucleic acid HPV target which has been amplified by the process of nucleic acid amplification of the invention.

The present invention relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample, by determination of whether at least one amplicon has been, or is produced from said sample, or from nucleic acid material thereof, by amplification by means of at least two amplification primers of the invention, and/or at least one amplification primer system of the invention.

The production of at least one amplicon indicates that at least one HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, is present in said sample.

According to an advantageous embodiment of the present invention, the determination of whether at least one amplicon is produced can be carried out in real-time multiplex amplification, preferably with at least one probe of the invention and/or at least one probe system of the invention.

The present invention thus relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample, which comprises:

-   -   contacting said sample, or nucleic acid material thereof, with         at least two amplification primers of the invention and/or at         least one primer system of the invention, under conditions         suitable to the production of at least one amplicon by said         primers (i.e., under conditions, which would be suitable to the         production by said primers of at least one amplicon from said at         least one HPV to be detected, if this HPV were present in said         sample),     -   determining whether at least one amplicon has been produced, or         is produced by said primers (e.g., by means of at least one         detection probe, preferably in real-time amplification involving         at least one probe of the invention and/or at least one         detection probe system of the invention).

The production of at least one amplicon indicates that at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially is oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, is present in said sample.

By “sample containing nucleic acid material”, it is meant any sample, which contains at least one nucleic acid, e.g., a biological sample, such as a sample which has been collected from a cell culture, or from an animal or a human being, e.g., from a female human being, preferably a sample which has been collected from a uterine cervix.

Said sample may optionally have been further treated and/or purified according to any technique known by the skilled person, to improve the amplification efficiency and/or qualitative accuracy and/or quantitative accuracy. The sample may thus exclusively, or essentially, consist of nucleic acid(s), whether obtained by purification, isolation, or by chemical synthesis. Means are available to the skilled person, who would like to isolate or purify nucleic acids, such as DNA, from a biological sample, for example to isolate or purify DNA from cervical scrapes (e.g., QIAamp-DNA Mini-Kit; Qiagen, Hilden, Germany).

Hence, the detection method of the present invention enables the real-time multiplex detection, preferably the real-time quantitative multiplex detection of:

at least the five most common HR HPV (i.e., HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18), more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53 still more preferably, at least the thirteen HPV as well as at least two among HPV to types 66, 82, 67, 85, and 53 even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53 most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85, still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53, in a single-tube assay.

The present invention also relates to all the medical, biological, pharmaceutical applications of the detection method of the invention, and/or of the primers and/or probes of the invention.

The present invention thus relates to a process for the diagnosis or prognosis of cervical neoplasia or cancer, which comprises determining the presence, re-occurrence, persistence, or cellular spread of at least one HPV by the detection method of the invention, e.g., by implementing it on a sample, which may have been collected from a patient, whereby a positive determination indicates that there is a cervical neoplasia or cancer, or that there is a prevalent risk of such a condition or disease.

The present invention also relates to a process for monitoring the efficiency of an anti-HPV treatment or drug, or an anti-HPV candidate treatment or drug, such as an anti-HPV16 and/or 18 and/or 45 treatment, drug, candidate treatment or candidate drug, which comprises determining said treatment, drug, candidate treatment or candidate drug induces the non-reoccurrence, non-persistence, disappearance, or a decrease in cellular spread of at least one HPV by the detection method of the invention, whereby a positive determination indicates that said treatment, drug, candidate treatment or candidate drug is an efficient anti-HPV drug.

The present invention also relates to a method to produce an anti-HPV drug, which comprises:

-   -   providing at least one anti-HPV candidate drug,     -   administering said at least one candidate anti-HPV drug to a         cell culture or to a non-human animal, wherein said cell culture         or animal is or comprises at least one cervical neoplasia or         cancer, and     -   determining by the HPV detection method of the invention whether         said candidate anti-HPV drug induces the regression or         disappearance of said at least one neoplasia or cancer,         whereby a positive determination indicates that said candidate         drug is an efficient anti-HPV drug.

As above-mentioned, the present invention thus provides HPV amplification and detection means, which can be implemented in real-time and in multiplex, i.e., which combine target amplification and detection in one single operative step, and which enables the detection of mucosal HPV in one single operative step, without any significant loss in specificity.

Furthermore, the amplification and detection systems of the invention have Ct and sensitivity levels, which are sufficiently homogeneous to allow for a real-time quantitative multiplex HPV detection.

According to the present invention, said amplification primers may comprise:

-   -   at least two primers, which are intended for targeting oncogenic         HPV of group A6, wherein said at least two A6-targeted primers         are oligonucleotides, which consist of 14-30 nucleotides,         preferably of 15-29, more preferably of 16-28, most preferably         of 17-25 nucleotides, the sequences of which are suitable for         use as forward and reverse primers, respectively, in the         amplification of at least one nucleic acid of 90-390         nucleotides, preferably of 95-385 nucleotides, more preferably         of 100-379 nucleotides, from the A6-target region consisting of         the E6 and E7 genes of HPV56, and/or     -   at least two primers, which are intended for targeting oncogenic         HPV of group A5, wherein said at least two A5-targeted primers         are oligonucleotides, which consist of 14-30 nucleotides,         preferably of 15-29, more preferably of 16-28, most preferably         of 17-25 nucleotides, the sequences of which are suitable for         use as forward and reverse primers, respectively, in the         amplification of at least one nucleic acid of at least 90-240         nucleotides, preferably of 100-230 nucleotides, more preferably         of 106-225 nucleotides, from the A5-target region consisting of         the E7 and E1 genes of HPV51, and/or     -   at least two primers, which are intended for targeting oncogenic         HPV of group A9, wherein said at least two A9-targeted primers         are oligonucleotides, which consist of 14-30 nucleotides,         preferably of 15-29, more preferably of 16-28, most preferably         of 17-25 nucleotides, the sequences of which are suitable for         use as forward and reverse primers, respectively, in the         amplification of at least one nucleic acid of at least 80-260         nucleotides, preferably of 85-250 nucleotides, more preferably         of 88-241 nucleotides, from the A9-target region consisting of         the E1 and E2 genes of each of the following group A9 HPV:         HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, preferably from the         E2 gene of each of said group A9 HPV, and/or     -   at least two primers, which are intended for targeting oncogenic         HPV of group A7, wherein said at least two A7-targeted primers         are oligonucleotides, which consist of 14-30 nucleotides,         preferably of 15-29, more preferably of 16-28, most preferably         of 17-25 nucleotides, the sequences of which are suitable for         use as forward and reverse primers, respectively, in the         amplification of at least one nucleic acid of at least 100-220         nucleotides, preferably of 120-215 nucleotides, more preferably         of 125-209 nucleotides, from the A7-target region consisting of         the E1 gene of each of the following group A7 HPV: HPV68, HPV39,         HPV59, HPV45, and HPV18.

The nucleic acid which is amplified from said A6 or A5 or A9 or A7 target region corresponds in said HPV to the nucleic acid sequence of the A6 or A5 or A9 or A7 reference template, respectively. Hence, these amplified nucleic acids usually have a high degree of identity with their respective reference template sequences, e.g., an identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 95%, over the entire length of said respective reference template sequence.

By nucleic acid, it herein preferably meant DNA.

Preferably, the at least two primers, which are intended for targeting one HPV group, are different from the at least two primers, which are intended for targeting the three other groups.

Said at least two A6-targeted primers may target a sequence, which is entirely within the E6 gene of each of said group A6 HPV (namely, HPV56), or which is entirely within the E7 gene of each of said group A6 HPV, or which overlap the E6 and E7 genes, for example with a forward primer targeting E6 and the reverse primer targeting E7, or conversely. Preferably, said at least two A6-targeted primers target a sequence, which overlap the E6 and E7 genes, for example with a forward primer targeting E6 and the reverse primer targeting E7, or conversely.

Said at least two A5-targeted primers may target a sequence, which is entirely within the E7 gene of each of said group A5 HPV (namely, HPV51), or which is entirely within the E1 gene of each of said group A5 HPV, or which overlap the E7 and E1 genes, for example with a forward primer targeting E7 and the reverse primer targeting E1, or conversely.

Said at least two A9-targeted primers may target a sequence, which is entirely within the E1 gene of each of said group A9 HPV (namely, of at least each of HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16), or which is entirely within the E2 gene of each of said group A9 HPV, or which overlap the E1 and E2 genes, for example with a forward primer targeting E1 and the reverse primer targeting E2, or conversely. In the examples given below, all A9 amplification systems target the E2 gene, except system C, which has a target that overlaps the E1 and E2 genes.

Said at least two A7-targeted primers may target a sequence, which is entirely within the E1 gene of each of said group A7 HPV (namely, within the E1 gene of at least each of HPV68, HPV39, HPV59, HPV45, HPV18).

In accordance with the present invention, said at least two A6-, A5-, A9- and A7-targeted primers notably share the specific technical feature of being suitable for use in a real-time (quantitative) multiplex detection of HPV, which can be oncogenic for the mucosal epithelia.

By “consisting of 14-30 nucleotides”, it is meant “consisting of 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides”.

The same applies mutatis mutandis to any range, which is recited in the present application.

The nucleotide lengths of the primers can be chosen independently from each other.

By oligonucleotide or primer, “the sequence of which is suitable for use in the amplification of” at least one HPV, or nucleic acid or sequence, it is meant that the sequence of the oligonucleotide or primer is such that they can hybridize to this HPV or nucleic acid or sequence, under conditions of moderate, but preferably high or very high stringency.

A primer of the invention may consist of a 14-30 nt oligonucleotide (preferably a 17-25 nt oligonucleotide), the sequence of which has an identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 92%, with a sequence of the same length contained in its group reference template sequence, most preferably with a sequence of the same length contained at the very 3′ end or at the very 5′ end of said group reference template sequence.

According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced can be carried out by using in real-time amplification at least one probe, preferably at least one A6-targeted probe and/or at least one at least one A5-targeted probe and/or at least one A9-targeted probe and/or at least one A7-targeted probe.

Preferably, said at least two A6-targeted primers are suitable for use in the amplification of more than one oncogenic HPV of group A6, namely at least HPV56 and at least one other oncogenic HPV of group A6 (e.g., HPV66, HPV53). According to the present invention, said at least two A6-targeted primers anneal to each of the group A6 HPV they target, in their E6 and/or E7 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A6-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E6 and E7 genes of each of the following group A6 HPV: HPV56 and HPV66. HPV66 is at present time not listed within the 13 HR HPV; some authors however consider that HPV66 could be a HR HPV.

Preferably, said at least two A5-targeted primers are suitable for use in the amplification of more than one oncogenic HPV of group A5, namely at least HPV51 and at least one other oncogenic HPV of group A5 (e.g., HPV82). According to the present invention, said at least two A5-targeted primers anneal to each of the group A5 HPV they target, in their E7 and/or E1 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A5-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E7 and E1 genes of each of the following group A5 HPV: HPV51 and HPV82.

Preferably, said at least two A9-targeted primers are suitable for use in the amplification of more than the six above-mentioned oncogenic HPV of group A9, namely at least HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, and at least one other oncogenic HPV of group A9 (e.g., HPV67). According to the present invention, said at least two A9-targeted primers anneal to each of the group A9 HPV they target, in their E1 and/or E2 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A9-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E1 and the E2 genes of each of the following group A9 HPV: HPV58, HPV33, HPV67, HPV52, HPV35, HPV31 and HPV16.

A group-targeted primer of the present invention may further target a HPV, which does not belong to the same group (as long as it does not target any group other than A6, A5, A7 or A9), i.e., an A9-targeted primer pair may target an HPV belonging to group A6 (such as HPV53), in addition to targeting the above-mentioned HPV of group A9. Hence, the respective sequences of said at least two A9-targeted primers may further be suitable for use as forward and reverse is primers in the amplification of at least one nucleic acid of HPV53.

Preferably, said at least two A7-targeted primers are suitable for use in the amplification of more than the five above-mentioned oncogenic HPV of group A7, namely at least HPV68, HPV39, HPV59, HPV45, and HPV18, and at least one other oncogenic HPV of group A7 (e.g., HPV85). According to the present invention, said at least two A7-targeted primers anneal to each of the group A7 HPV they target, in their E1 gene. Hence, according to an advantageous embodiment of the present invention, said at least two A7-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the E1 gene of each of the following group A7 HPV: HPV68, HPV39, HPV85, HPV59, HPV45, and HPV18.

To the best of the inventors' knowledge, there is no prior art multiplex process, which would allow the detection of a mucosal oncogenic HPV other than HPV56, HPV51, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, HPV68, HPV39, HPV59, HPV45, and HPV18. Until recently, these thirteen HPV were considered to be the 13 HR HPV (i.e., the 13 high risk HPV, i.e., the HPV which have the highest tumor prevalence). However, other HPV are now thought to belong to the HR HPV group, e.g., HPV66 and HPV53 (group A6). As prior art techniques, such as the HPV Amplicor test, are based on a global consensus design, additional HPV cannot be encompassed. On the contrary, the present invention is based on a design by group, and cover more than the 13 basic HR HPV, which is much safer for the patient, and which has the special advantage of being evolutive, in the sense that any oncogenic A6, A5, A9 and A7 new corner are likely to be taken into account.

Hence, to the best of the inventors' knowledge, the present invention has a mucosal oncogenic HPV spectrum, which is broadest than any other prior art technique, and has a bigger potential of adaptability to any evolution of HPV spectrum to be detected. The present invention therefore is safer than any other prior art technique.

The amplification primer systems of the invention preferentially amplify HPV that is belong to group A6 or A5 or A9 or A7, i.e., oncogenic HPV.

As above-mentioned, most of amplification primer systems of the invention are specific of the HPV set formed by groups A5 and A6 and A7 and A9, and more particularly are specific of the group to which they are targeted, i.e., most primer systems of the invention are specific of group A6 or A5 or A9 or A7 (and do not amplify any HPV of groups A11 or A4 or A3).

Hence, said at least two primers can advantageously be specific of the HPV set formed by groups A5 and A6 and A7 and A9, and more particularly of group A6, or group A5, or group A9, or group A7, preferably of the oncogenic HPV of group A6, or group A5, or group A9, or group A7.

Hence, according to a preferred embodiment of the present invention, said at least two primers can have such sequences that they are not suitable for use as forward and reverse primers in the amplification of any nucleic acid from an HPV, which would not belong to group A6, A5, A9 or A7. According to a more preferred embodiment of the present invention, the respective sequences of said at least two primers therefore are not suitable for use as forward and reverse primers in the amplification of a nucleic acid from an HPV, which is not oncogenic, preferably which is not oncogenic for the mucosal epithelia, more preferably which is not an anogenital HPV, most preferably which is not a cervical HPV.

In other words, said at least two primers preferably are specific of oncogenic HPV, compared to non-oncogenic HPV.

The present invention can be implemented in simplex, multi-tube simplex, in multiplex, as well as in multi-multiplex (“megaplex”). According to an advantageous embodiment of the present invention, said amplification can be a single-tube multiplex amplification, or a single-tube multi-multiplex amplification (“megaplex”).

By “single-tube multiplex amplification” or “multiplex amplification”, it is herein meant any amplification reaction aiming at the amplification, and optionally the detection, of more than one target in the same tube. For instance, multiplex amplification include duplex amplification (two targets), triplex amplification (three targets), as well as higher multiplex amplification. Multiplex amplification includes amplification reactions with more than one primer pair, for instance two primer pairs. In this case, there might be four different primers, but it is also possible for the two primer pairs to have one primer in common, e.g., the forward primer, and to have two distinct reverse primers. Multiplex amplification and detection also includes amplification reactions with a unique primer pair, but with more than one probe.

Hence, according to the multiplex embodiment of the present invention, more than one primer pair is present in the amplification reaction mixture. As a very advantageous embodiment of the present invention, at least four, preferably at least six, more preferably at least eight primer pairs can be present in the amplification reaction mixture. Indeed, the primers of the invention allow for a multiplex amplification, without any significant specificity loss. Hence, all reagents can be placed in the same tube to carry out the amplification assay on the sample to be tested, whereby whatever mucosal oncogenic HPV is present in this sample, it will be detected in a single-step procedure.

Preferably, said amplification primers comprise said at least two A6-targeted primers, and at least two primers selected from:

-   -   said at least two A5-targeted primers,     -   said at least two A9-targeted primers, and     -   said at least two A7-targeted primers.

Preferably, said amplification primers comprise said at least two A5-targeted primers, and at least two primers selected from:

-   -   said at least two A6-targeted primers, and/or     -   said at least two A9-targeted primers, and/or     -   said at least two A7-targeted primers.

Preferably, said amplification primers comprise said at least two A9-targeted primers, and at least two primers selected from:

-   -   said at least two A5-targeted primers, and/or     -   said at least two A6-targeted primers, and/or     -   said at least two A7-targeted primers.

Preferably, said amplification primers comprise said at least two A7-targeted primers, and at least two primers selected from:

-   -   said at least two A5-targeted primers, and/or     -   said at least two A9-targeted primers, and/or     -   said at least two A6-targeted primers.

Most preferably, said amplification primers comprise:

-   -   said at least two A6-targeted primers, and     -   said at least two A5-targeted primers, and     -   said at least two A9-targeted primers, and     -   said at least two A7-targeted primers.

According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced, is carried out by means of at least one probe, which is intended to anneal to said at least one amplicon, i.e., the sequence of the probe is sufficiently complementary to said at least one amplicon (or to the complementary sequence thereof) that the probe can anneal to said at least one amplicon, preferably under conditions of moderate, high or very high stringency.

The probe(s) of the invention can be implemented in any appropriate format. Preferably, the probe(s) of the invention is(are) not immobilized onto a solid support.

Most preferably, the probe(s) of the invention is(are) used in real-time amplification.

Hence, according to an advantageous embodiment of the present invention, said amplification can be a real-time amplification.

According to an advantageous embodiment of the present invention, said at least one probe is used in real-time amplification, i.e., said at least two primers and said at least two probes can be both present in the amplification reaction mixture, whereby said at least one probe anneal to the amplicon(s) produced by said at least two primers in real-time. In other words, the amplification and the detection can be carried out in a single step, namely in real-time amplification.

By real-time amplification, we hereby understand any amplification-based process allowing for monitoring of fluorescence emitted during the reaction as an indicator of amplicon production during each amplification cycle as opposed to the endpoint detection by conventional amplification process.

The present invention provides probes, which are intended to target the amplicon(s) obtainable by amplification of a mucosal oncogenic HPV nucleic acid by at least two A6- and/or A5- and/or A9- and/or A7-targeted primers.

These probes share the specific technical features of being suitable for use in a real-time multiplex amplification.

Some probes of the present invention allow to detect all the HPV of one group (i.e., they anneal to every amplicon that is obtainable by means of a group-targeted primer pair of the invention). Other probes of the present invention detect one or only some HPV of one group. Hence, the present invention further provides different levels of detection: the response can be a global detection of the presence or absence of at least one mucosal oncogenic HPV, or a more precise response, such as presence or absence of at least one mucosal oncogenic HPV of group A6 and/or A5 and/or A9 and/or A7, or an even more precise response such as presence or absence of at least one mucosal oncogenic HPV type(s).

Preferably, said determination of whether at least one amplicon is produced, is carried out by using in real-time amplification at least one A6- and/or A5- and/or A9- and/or A7-targeted probe, the sequence of which is suitable for use as a probe for the detection of at least one amplicon produced by said at least two A6- and/or A5- and/or A9- and/or A7-targeted primers, respectively.

According to an advantageous embodiment of the present invention, said amplification can be a real-time multiplex amplification.

According to a very advantageous embodiment of the present invention, said amplification can be carried out as a real-time multiplex amplification. Hence, the amplification reaction mixture can comprise more than two primers, and also at least one probe, without any significant loss of specificity in the detection of HPV. To the best of the inventors' knowledge, the present technique is the first to allow a real-time multiplex amplification. It is very advantageous, in the sense that any mucosal oncogenic HPV can be screened in a single tube assay, wherein all reactants (primers and probe(s)) have been poured. More particularly, the present invention provides A6-, A5, A9- and A7-targeted primers and probes, which can all be placed in the same reaction mixture, without any significant loss in specificity.

The present invention therefore is much easier-to-handle and much quicker than any prior art technique. It further limits the possibility of any experimental error or contamination in the sample analysis.

To the best of the inventors' knowledge, the present technique is the first to enable a real-time multiplex amplification, which allows to cover at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, and as above-mentioned, most preferably at least 18 oncogenic HPV (namely, at least the 13 HR and five other oncogenic HPV, i.e., HPV 66, 53, 82, 67, 85).

According to an advantageous embodiment of the present invention, said amplification can be a quantitative real-time multiplex amplification.

According to an even more advantageous embodiment of the present invention, said amplification can be carried out as a quantitative real-time multiplex amplification. Indeed, the primers and probes of the present invention have such a sequence that there is no loss in specificity and no loss in quantitative accuracy, even when they are implemented in real-time multiplex amplification.

To the best of the inventors' knowledge, the present technique is the first to enable a quantitative real-time multiplex amplification, which allows to cover at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, and as above-mentioned, most preferably at least 18 oncogenic HPV is (namely, at least the 13 HR and five other oncogenic HPV, i.e., HPV 66, 53, 82, 67, 85).

The invention thereby finds applications not only in the field of diagnostic, but also in the field of therapy evaluation, such as to monitor the efficiency of an anti-HPV treatment, or to evaluate the efficiency of an anti-HPV drug. To the best of the inventors' knowledge, such therapy-related applications were previously unattainable by any of the prior art process.

The present invention thus represents a technological breakthrough in the field of HPV monitoring.

Hence, said amplification can be a quantitative real-time multiplex amplification, which allows for the detection of one or several of HPV, which can be oncogenic for the mucosal epithelia, in a single-tube amplification run.

The present invention thereby allows for the real-time multiplex detection, preferably the real-time quantitative multiplex detection of:

at least the five most common HPV (HPV16, 18, 45, 31, 33) preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18), more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53 still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53 even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53 most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85, still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53, in a single-tube assay.

Preferably, the respective sequences of said at least two A6-targeted primers are suitable for use in the amplification of at least one reference template sequence, wherein said at least one reference template sequence is a fragment consisting of positions 413-791 (SEQ ID NO:337) of the HPV56 sequence of SEQ ID NO:420 (accession NC_(—)001594.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A6-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.

More preferably, the respective sequences of said at least two A6-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of one of SEQ ID NO:25-29 and NO:334-338, as shown in Table 18 (A6 reference templates); or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A6-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of is HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.

As the reference template sequence is defined as consisting of one of the above-mentioned SEQ ID NOs (and not as comprising one of the above-mentioned SEQ ID NOs), the primers do not flank these reference template sequences, but fall within the reference template sequence, in such a way that the amplicon consists of one of the listed SEQ ID NOs. Unless otherwise stated, it applies to any reference template sequence that is herein defined as consisting of a SEQ ID NO.

Said at least two A6-targeted primers can, for example, be at least one of SEQ ID NO: 30-34 (forward primer) and at least one of SEQ ID NO: 35-37 (reverse primer).

As illustrated by the examples below (see e.g., Table 23), preferred combinations of forward and reverse primers are as follows:

TABLE 1 (A6 primer systems): SEQ ID NO: 35 36 37 30 X X 31 X X 32 X X X 33 X X 34 X wherein X indicates that the primers can be combined with each other as a pair.

According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced by said at least one A6-targeted primer system, can be carried out by using in real-time amplification at least one probe, preferably at least one A6-targeted probe.

Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A6-targeted probe, which consists of one of SEQ ID NO:38-40, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one 5′ and/or 3′ detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or Scorpion™ arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.

As illustrated by the examples below (see e.g., table 23), preferred combinations of primer pair and probe are as follows:

TABLE 2 (A6 primer and probe systems): A6 amplification Primer pair At least one probe system SEQ ID NO: of SEQ ID NO: A 30; 35 38 AE 30; 37 38 and/or 40 B 31; 35 38 BE 31; 37 38 and/or 40 C 32; 36 39 CA 32; 35 38 and/or 39 CE 32; 37 38 and/or 39 and/or 40 D 33; 35 38 DE 33; 37 38 and/or 40 E 34; 37 40

Advantageously, said at least one A6-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO:41-45, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).

As illustrated by the examples below (see e.g., Table 23), most preferred combinations of primer pair and beacon probes are as follows:

TABLE 3 (A6 primer and beacon probe systems): A6 amplification Primer pair At least one beacon system SEQ ID NO: probe of SEQ ID NO: A 30; 35 41 AE 30; 37 41 and/or 44 and/or 45 B 31; 35 41 BE 31; 37 41 and/or 44 and/or 45 C 32; 36 42 and/or 43 CA 32; 35 41 and/or 42 and/or 43 CE 32; 37 41 and/or 42 and/or 43 and/or 44 and/or 45 D 33; 35 41 DE 33; 37 41 and/or 44 and/or 45 E 34; 37 44 and/or 45

Preferably, the respective sequences of said at least two A5-targeted primers are suitable for use in the amplification of at least one reference template sequence, which is a fragment consisting of positions 678-902 (SEQ ID NO:326) of the HPV51 sequence of SEQ ID NO:421 (accession NC_(—)001533.1), or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A5-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.

More preferably, the respective sequences of said at least two A5-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, wherein said at least one reference template sequence consists of one of SEQ ID NO: 1-5 and NO: 320-333, as shown in Table 12; or a sequence which is fully complementary thereto over the entire length of said SEQ ID sequence.

Said reference template sequences share the specific technical feature of being suitable references to construct and produce A5-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.

Said at least two A5-targeted primers may, for example, be at least one of SEQ ID NO: 6-10 (forward primer) and at least one of SEQ ID NO: 11-15 (reverse primer).

As illustrated by the examples below (see e.g., Table 17), preferred combinations of forward and reverse primers are as follows:

TABLE 4 (A5 primer systems): SEQ ID NO: 6 7 8 9 10 11 X X X X X 12 X X X X X 13 X 14 X X X X X 15 X X X wherein X indicates that the primers can be combined with each other as a pair.

Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A5-targeted probe, which consists of one of SEQ ID NO:16-19, or of one of the complementary is sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or Scorpion™ arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.

As illustrated by the examples below (see e.g., Table 17), preferred combinations of primer pair and probe are as follows:

TABLE 5 (A5 primer and probe systems): A5 amplification Primer pair At least one probe system SEQ ID NO: of SEQ ID NO: A 6; 11 16 AB 6; 12 16 AD 6; 14 16 B 7; 12 16; 17 BA 7; 11 16; 17 BD 7; 14 16; 17 C 8; 13 18 CA 8; 11 16; 17; 18; 19 CB 8; 12 16; 17; 18; 19 CD 8; 14 16; 17; 18; 19 CE 8; 15 18; 19 D 9; 14 16; 17; 19 DA 9; 11 16; 17; 19 DB 9; 12 16; 17; 19 DE 9; 15 19 E 10; 15  19 EA 10; 11  16; 17; 19 EB 10; 12  16; 17; 19 ED 10; 14  16; 17; 19

Advantageously, said at least one A5-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO: 20-24, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).

As illustrated by the examples below (see e.g., Table 17), most preferred combinations of primer pair and probe are as follows:

TABLE 6 (A5 primer and beacon probe systems): A5 amplification Primer pair At least one beacon system SEQ ID NO: probe of SEQ ID NO: A 6; 11 20; 21 AB 6; 12 20; 21 AD 6; 14 20; 21 B 7; 12 20; 21; 22 BA 7; 11 20; 21; 22 BD 7; 14 20; 21; 22 C 8; 13 23 CA 8; 11 20; 21; 22; 23; 24 CB 8; 12 20; 21; 22; 23; 24 CD 8; 14 20; 21; 22; 23; 24 CE 8; 15 23; 24 D 9; 14 20; 21; 22; 24 DA 9; 11 20; 21; 22; 24 DB 9; 12 20; 21; 22; 24 DE 9; 15 24 E 10; 15  24 EA 10; 11  20; 21; 22; 24 EB 10; 12  20; 21; 22; 24 ED 10; 14  20; 21; 22; 24

Preferably, the respective sequences of said at least two A9-targeted primers are suitable for use in the amplification of at least one reference template sequence, which is:

-   -   a fragment consisting of positions 2707-2794 (SEQ ID NO:122) of         the HPV16 sequence of SEQ ID NO:422 (accession NC_(—)001526.1);         or a conservative sub-fragment thereof, which has retained the         property of being a suitable reference template sequence, to         construct and produce A9-targeted primers, which allow for a         real-time multiplex detection of those HPV, which can be         oncogenic for the mucosal epithelia, preferably of at least the         five most common HPV (HPV16, 18, 45, 31, 33), still preferably         at least 7 HR HPV, even still preferably the five most common HR         HPV as well as at least two other HR HPV, advantageously at         least two other HR HPV belonging to groups A6 and/or A5 (e.g.,         HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13         HR HPV, most preferably at least the 13 HR HPV and at least one,         at least two, at least three, at least four, or the five of         HPV66, 53, 82, 67, 85; or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment or     -   a fragment consisting of positions 3600-3840 (SEQ ID NO:377) of         the HPV16 sequence of SEQ ID NO:422 (accession NC_(—)001526.1);         or a conservative sub-fragment thereof, which has retained the         property of being a suitable reference template sequence, to         construct and produce A9-targeted primers, which allow for a         real-time multiplex detection of those HPV, which can be         oncogenic for the mucosal epithelia, preferably of at least the         five most common HPV (HPV16, 18, 45, 31, 33), still preferably         at least 7 HR HPV, even still preferably the five most common HR         HPV as well as at least two other HR HPV, advantageously at         least two other HR HPV belonging to groups A6 and/or A5 (e.g.,         HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13         HR HPV, most preferably at least the is 13 HR HPV and at least         one, at least two, at least three, at least four, or the five of         HPV66, 53, 82, 67, 85; or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment.

More preferably, the respective sequences of said at least two A9-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of any one of SEQ ID NO: 122-210 and 359-419, as shown in Table 30; or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A9-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.

Said at least two A9-targeted primers can, for example, be at least one of SEQ ID NO: 211-239 (forward primers) and at least one of SEQ ID NO: 240-265 (reverse primers).

As illustrated by the examples below (see e.g., Table 35), preferred combinations of forward and reverse primers are as follows:

-   -   A9 amplification system C: at least one of SEQ ID NO:211-217 and         at least one of SEQ ID NO:240-241; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least three of SEQ ID NO: 211-217, e.g., 212, 214 and 216, and         both of SEQ ID NO:240-241;     -   A9 amplification system E1: at least one of SEQ ID NO:218-220         and at least one of SEQ ID NO:242-247; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:218-220 and at least five of SEQ ID         NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);     -   A9 amplification system E2: at least one of SEQ ID NO:221-223         and at least one of SEQ ID NO:242-247; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:221-223 and at least five of SEQ ID         NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);     -   A9 amplification system E3: at least one of SEQ ID NO:221-223         and at least one of SEQ ID NO:248-255; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:221-223 and at least five of SEQ ID         NO:248-255 (e.g., SEQ ID NO:248-252);     -   A9 amplification system E4: at least one of SEQ ID NO:224-226         and at least one of SEQ ID NO:248-255; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:224-226 and at least five of SEQ ID         NO:248-255 (e.g., SEQ ID NO:248-252);     -   A9 amplification system E5: at least one of SEQ ID NO:224-226         and at least one of SEQ ID NO:242-247; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:224-226 and at least five of SEQ ID         NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);     -   A9 amplification system E6: at least one of SEQ ID NO:218-220         and at least one of SEQ ID NO:248-255; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:218-220 and at least five of SEQ ID         NO:248-255 (e.g., SEQ ID NO:248-252);     -   A9 amplification system E1H Z7: at least one of SEQ ID         NO:218-220 and at least one of SEQ ID NO:256-259; 261-265;         preferably, when amplification of all oncogenic HPV of group A9         is desired, at least the three of SEQ ID NO:218-220 and at least         four of SEQ ID NO: 256-259; 261-265 (e.g., SEQ ID NO:258; 261;         264; 265);     -   A9 amplification system E1H Z8: at least one of SEQ ID NO:         218-220 and at least one of SEQ ID NO:256-259; 261-265;         preferably, when amplification of all oncogenic HPV of group A9         is desired, at least the three of SEQ ID NO:218-220 and at least         four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261;         264; 265);     -   A9 amplification system E2H Z7: at least one of SEQ ID         NO:221-223 and at least one of SEQ ID NO:256-259; 261-265;         preferably, when amplification of all oncogenic HPV of group A9         is desired, at least the three of SEQ ID NO:221-223 and at least         four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO: 258; 261;         264; 265);     -   A9 amplification system E2H Z8: identical to A9 amplification         system E2H Z7, i.e., at least one of SEQ ID NO:221-223 and at         least one of SEQ ID NO: 256-259; 261-265; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:221-223 and at least four of SEQ ID         NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);     -   A9 amplification system E4H Z7: at least one of SEQ ID         NO:224-226 and at least one of SEQ ID NO: 256-259; 261-265;         preferably, when amplification of all oncogenic HPV of group A9         is desired, at least the three of SEQ ID NO:224-226 and at least         four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261;         264; 265);     -   A9 amplification system E4H Z8: at least one of SEQ ID         NO:224-226 and at least one of SEQ ID NO: 256-259; 261-265;         preferably, when amplification of all oncogenic HPV of group A9         is desired, at least the three of SEQ ID NO:224-226 and at least         four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO: 258; 261;         264; 265);     -   A9 amplification system F: at least one of SEQ ID NO:227-230 and         at least one of SEQ ID NO:248-255; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the four of SEQ ID NO:227-230 and at least five of SEQ ID         NO:248-255 (e.g., SEQ ID NO:248-252);     -   A9 amplification system FE: at least one of SEQ ID NO:227-230         and at least one of SEQ ID NO:242-247; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the four of SEQ ID NO:227-230 and at least five of SEQ ID         NO:242-247 (e.g., SEQ ID NO:242-243; 245-247);     -   A9 amplification system FH Z7: at least one of SEQ ID NO:227-230         and at least one of SEQ ID NO:256-259; 261-265; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the four of SEQ ID NO:227-230 and at least four of SEQ ID         NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);     -   A9 amplification system FHZ8: identical to A9 amplification         system FH Z7, i.e., at least one of SEQ ID NO:227-230 and at         least one of SEQ ID NO:256-259; 261-265; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:227-230 and at least four of SEQ ID         NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);     -   A9 amplification system G Z7: at least one of SEQ ID NO:227-230         and at least one of SEQ ID NO:256-261; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least the three of SEQ ID NO:227-230 and at least five of SEQ ID         NO:256-261 (e.g., SEQ ID NO:257-261);     -   A9 amplification system G Z8: identical to A9 amplification         system G Z7, i.e., at least one of SEQ ID NO:227-230 and at         least one of SEQ ID NO:256-261; preferably, when amplification         of all oncogenic HPV of group A9 is desired, at least the three         of SEQ ID NO:227-230 and at least five of SEQ ID NO:256-261         (e.g., SEQ ID NO:257-261);     -   A9 amplification system H: at least one of SEQ ID NO:231-239 and         at least one of SEQ ID NO: 256-259; 261-265; preferably, when         amplification of all oncogenic HPV of group A9 is desired, at         least three of SEQ ID NO:231-239 (e.g., SEQ ID NO:232; 234; 235)         and at least four of SEQ ID NO: 256-259; 261-265 (e.g., SEQ ID         NO:258; 261; 264; 265).

Advantageously, said determination of whether at least one amplicon is produced to is carried out by using in real-time amplification at least one A9-targeted probe, which consists of one of SEQ ID NO: 266-282, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or Scorpion™ arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.

As illustrated by the examples below (see e.g., Table 35), preferred combinations of primer pair and probe are as follows:

TABLE 7 (A9 primer and probe systems): A9 amplification At least one probe system of SEQ ID NO: C 266-271 E1 272-276 E2 272-276 E3 272-276 E4 272-276 E5 272-276 E6 272-276 E1H Z7 272-276 E1H Z8 277-282 E2H Z7 272-276 E2H Z8 277-282 E4H Z7 272-276 E4H Z8 277-282 F 272-276 FE 272-276 FH Z7 272-276 FH Z8 277-282 G Z7 272-276 G Z8 277-282 H 277-282

Advantageously, said at least one A9-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO: 283-319, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).

As illustrated by the examples below (see e.g., Table 35), most preferred combinations of primer pair and probe are as follows:

TABLE 8 (A9 primer and beacon probe systems): A9 amplification At least one beacon system probe of SEQ ID NO: C 283-295 E1 296-303 E2 296-303 E3 296-303 E4 296-303 E5 296-303 E6 296-303 E1 H Z7 296-303 E1 H Z8 304-319 E2H Z7 296-303 E2H Z8 304-319 E4H Z7 296-303 E4H Z8 304-319 F 296-303 FE 296-303 FH Z7 296-303 FH Z8 304-319 G Z7 296-303 G Z8 304-319 H 304-319

Some of the specificity results of the above-mentioned probes are shown in Tables 60-68 (Specificity A9).

In all tables, when the name of a probe differs from the name of another probe by only the last letter (e.g., A9E1S10 and A9E1S10a), these probes have the same hybridizing segment, and only differ in their beacon arms.

Gray boxes indicate that the tested probe detects the amplicon.

For example, probe A9E1S11 of SEQ ID NO: 285 detects HPV31 and HPV35, without detecting the other HPV.

For example, probe A9E1S10a of SEQ ID NO: 284 detects all oncogenic HPV of group A9 (HPV16, 31, 33, 35, 52, 58, 67) and one HPV of group A6 (HPV53), and probe A9E1S12a of SEQ ID NO: 288 detects HPV31 and HPV35, without detecting HPV53 (“ND”). Hence, a combination of A9E1S10a and of A9E1S12a allows the specific detection of HPV16, 31, 33, 35, 52, 58, 67, 53.

Any combination that the skilled person may find appropriate is herein specifically encompassed.

Preferably, the respective sequences of said at least two A7-targeted primers are suitable for use in the amplification of at least one reference template sequence, wherein said at least one reference template sequence is:

-   -   a fragment consisting of positions 1895-2103 (SEQ ID NO:48) of         the HPV18 sequence of SEQ ID NO:423 (accession NC_(—)001357.1);         or a conservative sub-fragment thereof, which has retained the         property of being a suitable reference template sequence, to         construct and produce A7-targeted primers, which allow for a         real-time multiplex detection of those HPV, which can be         oncogenic for the mucosal epithelia, preferably of at least the         five most common HPV (HPV16, 18, 45, 31, 33), still preferably         at least 7 HR HPV, even still preferably the five most common HR         HPV as well as at least two other HR HPV, advantageously at         least two other HR HPV belonging to groups A6 and/or A5 (e.g.,         HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13         HR HPV, most preferably at least the 13 HR HPV and at least one,         at least two, at least three, at least four, or the five of         HPV66, 53, 82, 67, 85; or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment, or     -   a fragment consisting of positions 916-1044 (SEQ ID NO: 65) of         the HPV18 sequence of SEQ ID NO:423 (accession NC_(—)001357.1);         or a conservative sub-fragment thereof, which has retained the         property of being a suitable reference template sequence, to         construct and produce A7-targeted primers, which allow for a         real-time multiplex detection of those HPV, which can be         oncogenic for the mucosal epithelia, preferably of at least the         five most common HPV (HPV16, 18, 45, 31, 33), still preferably         at least 7 HR HPV, even still preferably the five most common HR         HPV as well as at least two other HR HPV, advantageously at         least two other HR HPV belonging to groups A6 and/or A5 (e.g.,         HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13         HR HPV, most preferably at least the 13 HR HPV and at least one,         at least two, at least three, at least four, or the five of         HPV66, 53, 82, 67, 85; or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment.

More preferably, the respective sequences of said at least two A7-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of one of SEQ ID NO:46-67; 339-358, as shown in Table 24; or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A7-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.

Said at least two A7-targeted primers can, for example, be at least one of SEQ ID NO: 68-78 (forward primer) and at least one of SEQ ID NO: 79-87 (reverse primer).

As illustrated by the examples below (see e.g., Table 29), preferred combinations of forward and reverse primers are as follows:

-   -   A7 amplification system A: at least one of SEQ ID NO:68-70 and         at least one of SEQ ID NO:79-81; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system A1: identical to A7 amplification system         A, i.e., at least one of SEQ ID NO:68-70 and at least one of SEQ         ID NO:79-81; preferably, when amplification of all oncogenic HPV         of group A7 is desired, all of them;     -   A7 amplification system A2: identical to A7 amplification system         A or A1, i.e., at least one of SEQ ID NO:68-70 and at least one         of SEQ ID NO:79-81; preferably, when amplification of all         oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system AB: at least one of SEQ ID NO:68-70 and         at least one of SEQ ID NO:82-83; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system AC1: at least one of SEQ ID NO:68-70 and         at least one of SEQ ID NO:84-85; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system AC2: identical to A7 amplification         system AC1, i.e., at least one of SEQ ID NO:68-70 and at least         one of SEQ ID NO:84-85; preferably, when amplification of all         oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system AC3: identical to A7 amplification         system AC1 or AC2, i.e., at least one of SEQ ID NO:68-70 and at         least one of SEQ ID NO:84-85; preferably, when amplification of         all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system B: at least one of SEQ ID NO:71-73 and         at least one of SEQ ID NO:82-83; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BA1: at least one of SEQ ID NO:71-73 and         at least one of SEQ ID NO:79-81; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BA2: identical to A7 amplification         system BA1, i.e., at least one of SEQ ID NO:71-73 and at least         one of SEQ ID NO:79-81; preferably, when amplification of all         oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BA3: identical to A7 amplification         system BA1 or BA2, i.e., at least one of SEQ ID NO:71-73 and at         least one of SEQ ID NO:79-81; preferably, when amplification of         all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BC1: at least one of SEQ ID NO:71-73 and         at least one of SEQ ID NO:84-85; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BC2: identical to A7 amplification         system BC1, i.e., at least one of SEQ ID NO:71-73 and at least         one of SEQ ID NO:84-85; preferably, when amplification of all         oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system BC3: identical to A7 amplification         system BC1 or BC2, i.e., at least one of SEQ ID NO:71-73 and at         least one of SEQ ID NO:84-85; preferably, when amplification of         all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system C: at least one of SEQ ID NO:74-76 and         at least one of SEQ ID NO:84-85; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system C1: identical to A7 amplification system         C, i.e., at least one of SEQ ID NO:74-76 and at least one of SEQ         ID NO:84-85; preferably, when amplification of all oncogenic HPV         of group A7 is desired, all of them;     -   A7 amplification system CA1: identical to A7 amplification         system C1, i.e., at least one of SEQ ID NO:74-76 and at least         one of SEQ ID NO:79-81; preferably, when amplification of all         oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system CA2: identical to A7 amplification         system C1 or CA1, i.e., at least one of SEQ ID NO:74-76 and at         least one of SEQ ID NO:79-81; preferably, when amplification of         all oncogenic HPV of group A7 is desired, all of them;     -   A7 amplification system D: at least one of SEQ ID NO:77-78 and         at least one of SEQ ID NO:86-87; preferably, when amplification         of all oncogenic HPV of group A7 is desired, all of them.

Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A7-targeted probe, which consists of one of SEQ ID NO:88-101, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or Scorpion™ arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.

As illustrated by the examples below (see e.g., Table 29), preferred combinations of primer pair and probe are as follows:

TABLE 10 (A7 primer and probe systems): At least one A7 amplification system probe of SEQ ID NO: A 88-92 A1 92-95 A2 89-91; 96 AB 92-95 AC1 88-92 AC2 92-95 AC3 89-91; 96 B 92-95 BA1 88-92 BA2 92-95 BA3 89-91; 96 BC1 88-92 BC2 92-95 BC3 89-91; 96 C 89-91; 96 C1 88-91; 96 CA1 89-91; 96 CA2 88-91; 96 D 97-101

Advantageously, said at least one A7-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO:102-121, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).

As illustrated by the examples below (see e.g., Table 29), most preferred combinations of primer pair and probe are as follows:

TABLE 11 (A7 primer and beacon probe systems): At least one beacon A7 amplification system probe of SEQ ID NO: A 102-106 A1 106-110 A2 105; 111-114 AB 106-110 AC1 102-106 AC2 106-110 AC3 105; 111-114 B 106-110 BA1 102-106 BA2 106-110 BA3 105; 111-114 BC1 102-106 BC2 106-110 BC3 105; 111-114 C 105; 111-114 C1 102-105; 114 CA1 105; 111-114 CA2 102-105; 114 D 115-121

Said amplification can be any nucleic acid amplification, which is found appropriate to the skilled person, for example a PCR (Polymerase Chain Reaction), or an isothermal amplification technique, e.g., TMA (transcription mediated amplification), NASBA (nucleic acid sequence based amplification), 3SR (self sustained sequence replication) or strand displacement amplification. Said amplification preferably is a PCR.

In a preferred embodiment, the primers according to the invention are used in a final concentration range 100-2000 nM. Typically, said primers can be used at a final concentration range 200-1500 nM, preferably 250-1000 nM, more preferably 500-1000 nM, even more preferably 600-1000 nM.

Probe concentration in a PCR reaction can be optimized, typically by varying the final concentration from 50 nM to 1000 nM. In a preferred embodiment, the probes is according to the invention are used at a final concentration range 50-1000 nM, preferably 100-800 nM, more preferably 100-600 nM, even more preferably 200-600 nM.

Appropriate amplification conditions are known to those skilled in the art. They include temperature conditions, in particular thermal cycling conditions, e.g. temperature, duration, number, heating rate of the cycles. In a preferred embodiment, said temperature conditions include conditions suitable for a PCR. In another preferred embodiment, said conditions include conditions suitable for a Q-PCR.

Any megaplex, i.e., multi-multiplex comprising at least A6-targeted one real-time amplification system of the invention and at least one A5-targeted one real-time to amplification system of the invention and at least one A9-targeted one real-time amplification system of the invention and at least one A7-targeted one real-time amplification system of the invention, which would be contemplated by the person of ordinary skill in the art is encompassed by the present application.

For example, the A5-targeted system E, and the A6-targeted system A, and the A7-targeted system A, and the A9-targeted system H, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EAAH”).

For example, the A5-targeted system E, and the A6-targeted system B, and the A7-targeted system A, and the A9-targeted system C, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBAC”).

Illustrative specificity and sensitivity results of such megaplex are shown in tables 83-88 below.

From tables 84 and 87 (“megaplex EAAH”), it can be seen that such a megaplex enable to efficiently detect the oncogenic HPV, namely the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85), and that this megaplex has sufficiently homogeneous sensitivity and specificity (Ct) results to be quantitative for at least the 13 HR HPV and four other oncogenic HPV (HPV66, 53, 82, 85). From tables 86 and 88 (“megaplex EBAC”), it can be seen that such a megaplex enable to efficiently detect the oncogenic HPV, namely at least the 13 HR HPV, and that this megaplex has sufficiently homogeneous sensitivity and specificity (Ct) results to be quantitative for at least the five most common HR HPV (HPV16, 18, 45, 31, 33).

Preferred megaplex notably comprise the above-mentioned EAAH and EBAC megaplex, as well as the following megaplex systems:

-   -   the combination of A5-targeted system E, and the A6-targeted         system B, and the A7-targeted system C, and the A9-targeted         system C, can be used together in a single-tube assay, thereby         forming a megaplex (“megaplex EBCC”);     -   the combination of A5-targeted system E, and the A6-targeted         system B, and the A7-targeted system B, and the A9-targeted         system C, can be used together in a single-tube assay, thereby         forming a megaplex (“megaplex to EBBC”);     -   the combination of A5-targeted system E, and the A6-targeted         system B, and the A7-targeted system D, and the A9-targeted         system C, can be used together in a single-tube assay, thereby         forming a megaplex (“megaplex EBDC”);     -   the combination of A5-targeted system E, and the A6-targeted         system B, and the A7-targeted system A, and the A9-targeted         system H, can be used together in a single-tube assay, thereby         forming a megaplex (“megaplex EBAH”).

The present application also relates to any amplicon obtainable by implementation of the process according to any one claims 1-45 on a HPV-containing sample, which contains at least one HPV of group A6, A5, A9 or A7, for example, a sample which contains HPV66 and/or HPV53 and/or HPV82 and/or HPV58 and/or HPV33 and/or HPV67 and/or HPV52 and/or HPV35 and/or HPV31 and/or HPV68 and/or HPV39 and/or HPV85 and/or HPV59 and/or HPV45.

The invention is also directed to a polynucleotide suitable for use as a reference template sequence in the design of primers that can be used in multiplex to cover:

at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18), more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53 still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53 even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53 most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85, still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53, in a single amplification run while still offering a real time quantitative amplification thereof.

Of course, the polynucleotides according to the present invention are also suitable is for further protocols, including simplex protocols, multiplex protocols, end-point protocols, qualitative protocols, quantitative protocols, combinations thereof, and the like.

By polynucleotide, we hereby understand any polymer of nucleotides, wherein nucleotides can be ribonucleotides, deoxyribonucleotides, dideoxyribonucleotides, degenerated nucleotides, and the like. Said nucleotides are preferably single-stranded, but can also be double stranded. The length of said polynucleotides can vary, and is usually under 500 nucleotides (nt), preferably in the range of 50-400 nt, more preferably 100-300 nt, even more preferably 80-260 nt.

The present application also relates to any polynucleotide suitable for use as a reference template sequence in the design of primers that can be used in a single-tube multiplex to amplify those HPV of groups A6, A5, A9 and A7, and in the design of probes that can be used in said single-tube multiplex for real-time detection of said amplified HPV, said reference template polynucleotide being selected from:

-   -   for group A6: a fragment consisting of positions 413-791 of the         HPV56 sequence of SEQ ID NO:420 (accession NC_(—)001594.1), or a         conservative sub-fragment thereof, or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment;     -   for group A5: a fragment consisting of positions 678-902 of the         HPV51 sequence of SEQ ID NO:421 (accession NC_(—)001533.1), or a         conservative sub-fragment thereof, or a sequence which is fully         complementary to said fragment or sub-fragment over the entire         length of said fragment or sub-fragment;     -   for group A9: a fragment consisting of positions 2707-2794 of         the HPV16 to sequence of SEQ ID NO:422 (accession         NC_(—)001526.1), or a conservative sub-fragment thereof, or a         sequence which is fully complementary to said fragment or         sub-fragment over the entire length of said fragment or         sub-fragment; or a fragment consisting of positions 3600-3840 of         the HPV16 sequence of SEQ ID NO:422 (accession NC_(—)001526.1),         or a conservative sub-fragment thereof, or a sequence which is         fully complementary to said fragment or sub-fragment over the         entire length of said fragment or sub-fragment;     -   for group A7: a fragment consisting of positions 1895-2103 of         the HPV18 sequence of SEQ ID NO:423 (accession NC_(—)001357.1),         or a conservative sub-fragment thereof, or a sequence which is         fully complementary to said fragment or sub-fragment over the         entire length of said fragment or sub-fragment; or a fragment         consisting of positions 916-1044 of the HPV18 sequence of SEQ ID         NO:423 (accession NC_(—)001357.1), or a conservative         sub-fragment thereof, or a sequence which is fully complementary         to said fragment or sub-fragment over the entire length of said         fragment or sub-fragment,     -   wherein said conservative fragment thereof have retained the         property of being a suitable reference template sequence, to         construct and produce group-targeted primers, which allow for a         real-time multiplex detection of those HPV, which can be         oncogenic for the mucosal epithelia.

The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO:25-29 and NO:334-338 (group A6-targeted reference template polynucleotides), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: 1-5 and NO:320-333 (group A5-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: SEQ ID NO:122-210 and 359-419 (group A9-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: 46-67; 339-358 (group A7-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.

Conservative variants of the reference template polynucleotide of the invention are also encompassed by the present application. Conservative variants of a given parent reference template polynucleotide notably include any polynucleotide, which derives from said parent reference template polynucleotide, or the sequence which is fully complementary thereto, by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being a reference template polynucleotide for designing and building an A5- and/or A6- and/or A7- and/or A9-targeted primer pair enabling the amplification of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those polynucleotides, which have a sequence identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 95%, with said parent reference template polynucleotide or with the sequence which is fully complementary thereto (said identity score being computed over the entire length of said parent reference template polynucleotide, or fully complementary sequence). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.

The present application also relates to the primers and probes of the present invention, as such, i.e., as individual oligonucleotide products.

Conservative variants of the primers of the invention are also encompassed by the present application. Conservative variants of a given parent primer notably include any oligonucleotide, which derives from said parent primer by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being a forward or reverse A5- and/or A6- and/or A7- and/or A9-targeted primer for the amplification of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those oligonucleotides, which have a sequence identity of at least 80%, is preferably of at least 81%, more preferably of at least 83%, most preferably of least 85%, with said parent primer (said identity score being computed over the entire length of said parent primer). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.

Conservative variants of the probes of the invention are also encompassed by the present application. Conservative variants of a given parent probe notably include any oligonucleotide, which derives from said parent probe, or the sequence which is fully complementary thereto, by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being an A5- and/or A6- and/or A7- and/or A9-targeted probe for the detection of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those oligonucleotides, which have a sequence identity of at least 90%, preferably of at least 91%, more preferably of at least 93%, most preferably of at least 95%, with said parent probe or with the sequence which is fully complementary thereto (said identity score being computed over the entire length of said parent probe). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.

The present application more particularly relates to primers, which are suitable for HPV amplification, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.

Said primer can e.g., be:

-   -   an A6-targeted primer, consisting of any one of SEQ ID NO: 30-34         and SEQ ID NO: 35-37; or

an A5-targeted primer, consisting of any one of SEQ ID NO: 6-10 and SEQ ID NO: 11-15; or

-   -   an A9-targeted primer, consisting of any one of SEQ ID NO:         211-239 and SEQ ID NO: 240-265; or     -   an A7-targeted primer, consisting of any one of SEQ ID NO: 68-78         and SEQ ID NO: 79-87.

The present application more particularly relates to primer systems suitable for HPV amplification, which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.

Said primer system may e.g., be:

-   -   at least one A6-targeted primer consisting of one of SEQ ID NO:         30-34, and at least one A6-targeted primer consisting of one of         SEQ ID NO: 35-37; and/or     -   at least one A5-targeted primer consisting of one of SEQ ID NO:         6-10, and at least one A5-targeted primer consisting of one of         SEQ ID NO: 11-15; and/or     -   at least one A9-targeted primer consisting of one of SEQ ID NO:         211-239, and at least one A9-targeted primer consisting of one         of SEQ ID NO: 240-265; and/or     -   at least one A7-targeted primer consisting of one of SEQ ID NO:         68-78, and at least one A7-targeted primer consisting of one of         SEQ ID NO: 79-87.

The present application more particularly relates to probes, which are suitable for HPV detection, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.

Said probe may e.g., be:

-   -   an A6-targeted probe, consisting of any one of SEQ ID NO:38-40,         or a sequence which is fully complementary thereto over the         entire length of said SEQ ID NO sequence; or     -   an A5-targeted probe, consisting of any one of SEQ ID NO:16-19,         or a sequence which is fully complementary thereto over the         entire length of said SEQ ID NO sequence; or     -   an A9-targeted probe, consisting of any one of SEQ ID NO:         266-282, or a sequence which is fully complementary thereto over         the entire length of said SEQ ID NO sequence; or     -   an A7-targeted probe, consisting of any one of SEQ ID NO:88-101,         or a sequence which is fully complementary thereto over the         entire length of said SEQ ID NO sequence.

Said probes can be produced in various format, e.g., including Taqman™ probes (hydrolysis probes), Molecular Beacons™ (beacon probes or molecular beacon probes), and Scorpion™ probes. One of preferred formats is the beacon format. Hence, the present application more particularly relates to beacon probes, which is are suitable for HPV detection, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.

Said beacon probe may e.g., be:

-   -   an A6-targeted probe, consisting of any one of SEQ ID NO:41-45,         or a sequence which is fully complementary thereto over the         entire length of said SEQ ID NO sequence; or     -   an A5-targeted probe, consisting of any one of SEQ ID NO:20-24,         or a sequence which is fully complementary thereto over the         entire length of said SEQ ID NO sequence; or     -   an A9-targeted probe, consisting of any one of SEQ ID NO:         283-319, or a sequence which is fully complementary thereto over         the entire length of said SEQ ID NO sequence; or     -   an A7-targeted probe, consisting of any one of SEQ ID         NO:102-121, or a sequence which is fully complementary thereto         over the entire length of said SEQ ID NO sequence.

Beacon probe may further comprise a quencher and a reporter (e.g., a fluorophore).

Preferably, each probe has its own reporter, whereby each probe has a reporter that is different from the ones displayed by the other probes, whereby each probe can be easily distinguished from the other probes.

The present application more particularly relates to primer and probe systems, which are suitable for HPV amplification, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.

Said primer and probe system comprises at least one primer system according to the invention, and at least one probe according to the invention.

The present application further relates to any amplicon obtainable by amplification of at least one nucleic acid from an HPV of group A6, A5, A9 or A7, by means of at least one primer system according to claim 53, for example, HPV66 and/or HPV53 and/or HPV82 and/or HPV58 and/or HPV33 and/or HPV67 and/or HPV52 and/or HPV35 and/or HPV31 and/or HPV68 and/or HPV39 and/or HPV85 and/or HPV59 and/or HPV45.

An amplification composition comprising such an amplicon is also encompassed by the present invention.

The present invention also relates to an amplification composition, a pharmaceutical composition, a biological composition, comprising at least one primer or probe of the invention.

The present invention also relates to a kit for the diagnostic or prognostic of a cervical neoplasia or cancer, comprising:

-   -   at least one primer system according to the invention, and/or     -   at least one probe according to the invention,     -   optionally, instructions for the use thereof and/or nucleotides.

Preferably, said kit comprises at least two primer systems according to the invention, more preferably at least three primer systems according to the invention, most preferably at least four primer systems according to the invention. Said kit comprises more than one probe, e.g. at least two, at least three, at least four, at least five different probes, notably when the kit is intended to discriminate between different HPV types.

In the kit according to the invention, the oligonucleotides (primers, probes) can be either kept separately, or partially mixed, or totally mixed.

Said oligonucleotides can be provided under dry form, or solubilized in a suitable solvent, as judged by the skilled person. Suitable solvents include TE, PCR-grade water, and the like.

In a preferred embodiment, the kit according to the invention can also contain further reagents suitable for a PCR step.

Such reagents are known to those skilled in the art, and include water, like nuclease-free water, RNase free water, DNAse-free water, PCR-grade water; salts, like magnesium, potassium; buffers such as Tris; enzymes, including polymerases, such as Taq, Vent, Pfu (all of them Trade-Marks), activable polymerase, and the like; nucleotides like deoxynucleotides, dideoxunucleotides, dNTPs, dATP, dTTP, dCTP, dGTP, dUTP; other reagents, like DTT and/or RNase inhibitors; and polynucleotides like polyT, polydT, and other oligonucleotides, e.g., primers.

In another preferred embodiment, the kit according to the invention comprises PCR controls. Such controls are known in the art, and include qualitative controls, positive controls, negative controls, internal controls, quantitative controls, internal quantitative controls, as well as calibration ranges. The internal control for said PCR step can be a template which is unrelated to the target template in the PCR step. Such controls also may comprise control primers and/or control probes. For example, in the case of HPV detection, it is possible to use as an internal control, a polynucleotide chosen within a gene whose presence is excluded in a sample originating from a human body (for example, from a plant gene), and whose size and GC content is equivalent to those from the target sequence.

In a preferred embodiment, the kit according to the invention contains means for extracting and/or purifying nucleic acid from a biological sample, e.g. from blood, serum, plasma. Such means are well known to those skilled in the art.

In a preferred embodiment, the kit according to the invention contains instructions for the use thereof. Said instructions can advantageously be a leaflet, a card, or the like. Said instructions can also be present under two forms: a detailed one, gathering exhaustive information about the kit and the use thereof, possibly also including literature data; and a quick-guide form or a memo, e.g., in the shape of a card, gathering the essential information needed for the use thereof.

In a preferred embodiment, said kit is a diagnostics kit, especially an in vitro diagnostics kit, i.e., an HPV diagnostics kit.

The present invention also relates to the field of diagnostics, prognosis and drug/treatment efficiency monitoring, as above-described.

The oligonucleotides according to the present invention can be used for the diagnostic of HPV group, types, subtypes or strains. In particular, the primers and probes according to the invention can be used for in vitro typing, sub-typing, and quantification of HPV nucleic acids present in an in vitro sample, for instance, in a to patient's cervical sample, or in a cell culture supernatant.

The term “comprising”, which is synonymous with “including” or “containing”, is open-ended, and does not exclude additional, unrecited element(s), ingredient(s) or method step(s), whereas the term “consisting of” is a closed term, which excludes any additional element, step, or ingredient which is not explicitly recited. The term “essentially consisting of” is a partially open term, which does not exclude additional, unrecited element(s), step(s), or ingredient(s), as long as these additional element(s), step(s) or ingredient(s) do not materially affect the basic and novel properties of the invention.

The term “comprising” (or “comprise(s)”) hence includes the term “consisting of” (“consist(s) of”), as well as the term “essentially consisting of” (“essentially consist(s) of”). Accordingly, the term “comprising” (or “comprise(s)”) is, in the present application, meant as more particularly encompassing the term “consisting of” (“consist(s) of”), and the term “essentially consisting of” (“essentially consist(s) of”).

In the present application, the term “at least x” relating to a set or group of n elements (wherein x is different from zero, and n is a number that is higher than x), explicitly encompasses each value, which is comprises between x and n. For example, the term “at least one” relating to a group or set of six elements explicitly encompasses one, two, three, four, five and six of said elements, as well as at least two, at least three, at least four, at least five of said elements.

Each of the relevant disclosures of all references cited herein is specifically incorporated by reference. The following examples are offered by way of illustration, and not by way of limitation.

DEFINITIONS

The terms and names used in the present application have their ordinary meaning in the field of HPV detection in general, and of molecular biology in particular.

By <<amplification>>, it is meant any technique of nucleic acid amplification, such as the PCR (Polymerase Chain Reaction), or the isothermal amplification techniques, e.g., TMA (transcription mediated amplification), NASBA (nucleic acid sequence based amplification), 3SR (self sustained sequence replication) or strand displacement amplification.

Amplification methods, especially PCR-based methods, are known in the art (Molecular Cloning: A Laboratory Manual, Maniatis, Fritsch, and Sambrook, CSHL Press; Molecular Biology of the Cell, Alberts et al.; PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, CSHL Press; The Polymerase Chain Reaction, Mullis, Ferré, and Gibbs, Birkhauser Boston Press; Gene quantification, Ferré, Birkhauser Boston Press).

By PCR or PCR reaction, we hereby understand any PCR-based method. This includes standard PCR, qualitative, quantitative and semi-quantitative PCR, real-time PCR, reverse-transcriptase PCR (RT-PCR), simplex and multiplex PCR, and the like.

By real-time PCR, we hereby understand any PCR-based method allowing for monitoring of a signal, such as fluorescence, emitted during the reaction as an indicator of amplicon production during each PCR cycle as opposed to the endpoint detection by conventional PCR methods.

By quantitative PCR, we hereby understand any PCR-based method allowing for the estimation of the initial amount of a given PCR target in a given sample.

By multiplex PCR, we hereby understand any PCR reaction aiming at the amplification of more than one target. For instance, multiplex PCR include duplex PCR (two targets), triplex PCR (three targets), and higher multiplex PCR. Multiplex PCR includes PCR reactions with more than one primer pair, for instance two primer pairs. In this case, there might be four different primers, but it is also possible for the two primer pairs to have one primer in common, e.g. the forward primer, and to have two distinct reverse primers. Multiplex PCR also includes PCR reactions with a unique primer pair, but with more than one probe. The term “megaplex” is herein sometimes used: it basically has the same meaning as “multiplex”, but is used to distinguish multi-multiplex, which involves at least two different group-targeted systems (e.g., an A5- and an A6- and an A7- and an A9-targeted systems), from the “multiplex”, which involve one group-targeted system (e.g., an A7- or an A9-targeted system).

By nucleic acid, we hereby understand any nucleic acid: it can be synthetic or not, recombinant or naturally occurring, linear or circular. This includes DNA and RNA. The nucleic acid can be either single stranded or double stranded or even triple stranded. It can stem from various biological sources, such as micro organisms (bacteria, yeasts, and the like), or higher organisms, like mammal cells. Said nucleic acid can also be of viral nature, e.g., the HPV nucleic acids. The nucleic acid can also comprise total DNA, total RNA, genomic DNA, mitochondrial DNA, plasmidic DNA, BAC DNA, and mixtures thereof. Moreover, the nucleic acid can assume various states of purity.

By oligonucleotide, we hereby understand any short polymer of nucleotides, wherein nucleotides can be ribonucleotides, deoxyribonucleotides, dideoxyribonucleotides, degenerated nucleotides, and the like. Said oligonucleotides are preferably single-stranded. The length of said oligonucleotides can vary, and is usually under 150 nucleotides (nt), preferably in the range of 10-100 nt, more preferably 13-60 nt, even more preferably 13-50 nt. Said oligonucleotides can bear chemical modifications, such as tagging or marking, for instance radioactive, fluorescent, biotinylated, dig labelling. An oligonucleotide according to the invention can be either forward (sense) or reverse (antisense). In addition, it should be stressed, that although preferred functions may be mentioned in relation to some oligonucleotides according to the present invention, it is obvious that a given oligonucleotide may assume several functions, and may be used in different ways according to the present invention. For example, an oligonucleotide can be used either as a primer, or as a probe. Also, when an oligonucleotide is described as being useful as an amplicon-targeting probe, the skilled person understands that the complementary sequence of this oligonucleotide is equally useful as a probe to target the same amplicon. Moreover, it is also obvious, that any primer suitable for a multiplex assay, can also, within the meaning of the present invention, be used in a simplex protocol. The same applies to a primer suitable for a real-time protocol, which can also be used in the framework of an end-point assay within the meaning of the present invention.

Oligonucleotides according to the invention especially include PCR primers and probes. Unless otherwise stated, nucleic acid sequences are given in the 5′ to 3′ is direction. Said oligonucleotides can be under many forms, e.g. under dry state, in solution/suspension with the desired solvent and the desired concentration. The skilled person would know, which solvents, concentrations, storage conditions are suitable for the oligonucleotides of the invention. In particular, the skilled person would know how to prepare said oligonucleotides as stock solutions. The oligonucleotides according to the invention can also assume various degrees of purity, as can be judged by those skilled in the art, e.g., by HPLC chromatography.

By set or systems of oligonucleotides, we hereby understand any combination comprising at least one oligonucleotide, preferably at least two, e.g. 2-10 oligonucleotides. Said set can thus comprise one PCR primer, or a pair of PCR primers, or a probe, or a probe and a pair of primers. Said oligonucleotides can be separately kept, or partially mixed, or entirely mixed.

The notion of primer or PCR primer is known to those skilled in the art. For example, it includes any oligonucleotide able to anneal to a target template under suitable stringency conditions, and allowing for polymerase strand elongation. The typical length of said primer is 13-30 nt, preferably 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nt.

The terms “primer”, “amplification primer” or “nucleic acid primer” are used interchangeably herein. A “primer” refers to a short polynucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a polymerase and at a suitable temperature and pH. The primer must be sufficiently long to prime the synthesis of the desired extension product. The exact length of the primer will depend upon to experimental factors, and notably upon temperature, source of primer and use of the process.

A primer pair consists of a forward primer and a reverse primer, wherein the forward primer is sufficiently complementary to one HPV strand to hybridize thereto, and the reverse primer is sufficiently complementary to the other HPV strand to hybridize thereto.

Stringency refers to hybridization conditions chosen to optimize binding of polynucleotide sequences with different degrees of complementarity. Stringency is affected by factors such as temperature, salt conditions, the presence of organic solvents in the hybridization mixtures, and the lengths and base compositions of the sequences to be hybridized and the extent of base mismatching, and the combination of parameters is more important than the absolute measure of any one factor.

Very High Stringency: Very high stringency conditions refers to hybridization to filter-bound DNA in 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.1×SSC and 0.1% SDS at 60-65° C. for thirty minutes.

High Stringency High stringency conditions refers to hybridization to filter-bound DNA in 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.2×SSC and 0.2% SDS at 60-65° C. for thirty minutes.

Moderate Stringency Moderate stringency conditions refers to hybridization to filter-bound DNA in 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.2×SSC and 0.2% SDS at 50-55° C. for thirty minutes.

The notion of probe is also known to those skilled in the art. For example, it includes any oligonucleotide able to anneal to a target template under the desired hybridization conditions. The typical length of said probe is 15-60 nt, preferably 16-50 nt, more preferably 17-40 nt, more preferably 17-35 nt, more preferably 20-30 nt. Preferably, said probe is fluorescently labelled. However, it is clear to those skilled in the art that under certain conditions, one may use a primer as a probe and vice-versa. Moreover, it is herein stressed that the products according to the present invention, especially, inter alia, oligonucleotides, are not limited to the intended use herein mentioned, but rather are to be broadly construed, irrespective of the indicated destination. For instance, a claim to a product (oligonucleotide) for a particular use should be construed as meaning a product is (oligonucleotide) which is in fact suitable for the stated use. Thus, an oligonucleotide suitable for use as a primer in a multiplex protocol is also clearly adapted to a simplex protocol within the meaning of the present invention.

A probe may entirely consist of a hybridizing segment. By “hybridizing segment” or “annealing segment” of a probe, it is meant the nucleotide sequence, which is intended to anneal to the HPV target(s).

Alternatively, a probe may comprise at least one detection component, e.g. at least one detection label (such as a radioactive element, or a fluorophore). This detection label can be linked to the hybridizing segment of the probe via short HPV-unrelated oligonucleotide arms, which are known to the skilled person as beacon arm, or Scorpion™ arm. A probe, which comprises at least one 5′ and/or 3′ detection label, or at least one 5′ and/or 3′ beacon arm, consists of a hybridizing segment and of at least one 5′ and/or 3′ label or beacon arm.

Various formats (types) of probes, including Taqman™ probes (hydrolysis probes), Molecular Beacons™ (beacon probes or molecular beacon probes), and Scorpion™ probes are known in the art.

In a preferred embodiment, the probes according to the invention can all be synthesized and used in the molecular beacon format.

The structure of molecular beacons is as follows. A short nucleotide sequence (so-called beacon arm) which is unrelated to the target sequence is thus covalently linked to both ends of the probe. A short unrelated arm is thus linked in 5′ of the probe, and is labelled with a fluorescent moiety (i.e. fluorescent dye or fluorescent marker). Another but still unrelated arm is linked to the 3′ end of probe and is labelled with a fluorescence quenching moiety. Thus, molecular beacons have a fluorophore and a quencher at opposite ends. The 5′ short arm is totally complementary to the one in 3′ so that they can anneal together, and thus can assume a hairpin structure when unhybridized to the target in solution. In this hairpin conformation, the quencher and the fluorescent dye are close enough to each other to allow efficient quenching of the fluorophore. However, when the probe encounters a target molecule, annealing is favoured with respect to the hairpin conformation when values of beacon arm Tm and probe Tm are suitably chosen (theoretically: probe Tm>beacon arm Tm>primer Tm, wherein Tm is the melting temperature of interest). The fluorophore and quencher move away from each other and the fluorophore can then fluoresce when illuminated by suitable light excitation. As PCR proceeds, amplification product accumulates, and the amount of fluorescence at any given cycle depends on the amount of amplification product present at that time. (See e.g., Sanjay Tyagi and Fred Russell Kramer, Nature Biotechnology 1996, volume 14, pages 303-308; Nature Biotechnology 1998, volume 16, pages 49-53).

(Remark: It is also possible to link the fluorophore at the 3′ end, while attaching the quencher at the 5′ end.)

Schematically, said probe can have the following formulae (molecular beacon format):

5′ Fluorophore-(arm1)-probe-(arm2)-Quencher 3′ 5′ Quencher-(arm1)-probe-(arm2)-Fluorophore 3′ wherein arm1 and arm2 can be any short nucleotide sequences, e.g. in the range of 3-10 nucleotides, preferably 5, 6, 7 nucleotides, allowing for the hair pin structure formation under suitable stringency conditions, i.e. arm1 and arm2 are totally complementary to anneal under the desired stringency conditions (standard PCR stringency conditions include, for example, an annealing temperature of 55 to 65° C. and an Mg concentration of 4 to 8 mM). However, arm1 and arm2 are unrelated to the target sequence of the probe, i.e. the hairpin conformation resulting from the annealing between arm1 and arm2 is essentially the only possible secondary structure for the probe when unhybridized. The skilled person would know how to choose such arms for a given probe.

Illustrative beacon formats include:

TGCGC-(probe sequence)-GCGCA GCGCA-(probe sequence)-TGCGC AGCGC-(probe sequence)-GCGCT GCGCT-(probe sequence)-AGCGC CGCGA-(probe sequence)-TCGCG CGCGC-(probe sequence)-GCGCG.

By fluorophore, it is herein understood any fluorescent marker/dye known in the art. Examples of such suitable fluorescent markers include Fam, Hex, Tet, Joe, Rox, Tamra, Max, Edans, Cy dyes such as Cy5, Fluorescein, Coumarin, Eosine, Rhodamine, Bodipy, Alexa, Cascade Blue, Yakima Yellow, Lucifer Yellow and Texas Red (all of them are Trade-Marks), the family of ATTO dyes.

By quencher, we herein understand any quencher known in the art. Examples of such quenchers include Dabcyl, Dark Quencher, Eclipse Dark Quencher, ElleQuencher, Tamra, BHQ and QSY (all of them are Trade-Marks).

The skilled person would know which combinations of dye/quencher are suitable when designing a probe.

In a preferred embodiment according to the invention, spectral properties of said probes can be chosen as to not interfere with each other. In particular, when probes are used in multiplex, each single probe can have its own fluorophore being spectrally significantly different from each other, i.e. the absorption/emission spectra are essentially non-overlapping. This advantageously allows for low-noise multiplex detection for all single probes, making sure that individual signals do not interfere with each other in detection. Examples of dyes which can be used together in multiplex include Fam with Tamra, Fam with Tamra with Texas Red. The choice of appropriate dyes to be used together may also be dependent of the filter contained in the amplification apparatus.

According to the invention, all the provided oligonucleotides can be either kept separately, or partially mixed, or totally mixed.

Said oligonucleotides can be provided under dry form, or solubilized in a suitable solvent, as judged by the skilled person. Suitable solvents include TE, PCR-grade water, and the like.

The term “significantly” is herein used in its usual meaning in the field of statistics (e.g., t test, z test, chi squared value, or F ratio, etc.), i.e., for comparing a value to another one, and determining whether these values differ from each other. The term “significantly” hence encompasses the fact that the skilled person may take into account the standard deviation (if any), which measures the amount of spread to of data in a frequency distribution. The desired p value is usually set at an alpha level of 5%, or at the more stringent alpha level of 1%.

In the examples below, are described several A6-, A5-, A9 and A7-targeted amplification and/or detection systems of the invention.

Tables 12-35: these tables give the SEQ ID NO: and positions of the reference amplicons, the forward primers, the reverse primers, the probes, the beacons probes of illustrative group-targeted systems of the invention. Table 12: Reference amplicons of A5-targeted systems (from HPV51 genome) Table 13: Forward primers of A5-targeted systems Table 14: Reverse primers of A5-targeted systems Table 15: Probes of A5-targeted systems Table 16: Beacon probes of A5-targeted systems Table 17: A5-targeted systems Table 18: Reference amplicons of A6-targeted systems (from HPV56 genome) Table 19: Forward primers of A6-targeted systems Table 20: Reverse primers of A6-targeted systems Table 21: Probes of A6-targeted systems Table 22: Beacon probes of A6-targeted systems Table 23: A6-targeted systems Table 24: Reference amplicons of A7-targeted systems (from HPV18 genome) Table 25: Forward primers of A7-targeted systems Table 26: Reverse primers of A7-targeted systems Table 27: Probes of A7-targeted systems Table 28: Beacon probes of A7-targeted systems Table 29: A7-targeted systems Table 30: Reference amplicons of A9-targeted systems (from HPV16 genome) Table 31: Forward primers of A9-targeted systems Table 32: Reverse primers of A9-targeted systems Table 33: Probes of A9-targeted systems Table 34: Beacon probes of A9-targeted systems Table 35: A9-targeted systems Tables 36-50: these tables show the number of nucleotide mismatches shown by primers and probes of the invention (alignment of the sequences of 50 HPV types); an empty box indicates there is no coherent sequence alignment; a gray box indicates that the number of mismatch(es) is of 0, 1, 2 or 3. Table 36: mismatch numbers shown by primers and probes of A5-targeted systems of the invention (systems A to C) Table 37: mismatch numbers shown by primers and probes of A5-targeted systems of the invention (systems D to E) Table 38: mismatch numbers shown by primers and probes of A6-targeted systems of the invention (systems A to C) Table 39: mismatch numbers shown by primers and probes of A6-targeted systems of the invention (systems D to E) Table 40: mismatch numbers shown by primers and probes of A7-targeted systems of the invention (systems A to B) Table 41: mismatch numbers shown by primers and probes of A7-targeted systems of the invention (systems C to D) Table 42: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system C) Table 43: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E1) Table 44: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E2) Table 45: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E3) Table 46: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E4) Table 47: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system F) Table 48: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system GZ7) Table 49: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system GZ8) Table 50: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system H) Tables 51-68: specificity of the detection systems of the invention

The amplification systems described in tables 36-50 have been used to test the specificity of the probes of the invention.

Table 51: illustrative list of HPV plasmids, which can be used to test the HPV specificity of the detection systems of the invention; the whole list of plasmids have been used for the specificity results, which are herein described Table 52: illustrative PCR material and method conditions, which can be used to test the specificity of the A5- and A6-targeted detection systems of the invention Table 53: specificity results of A5-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51) Table 54: specificity results of A6-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51) Table 55: illustrative PCR material and method conditions, which can be used to test the specificity of the A7-targeted detection systems of the invention Tables 56-59: specificity results of A7-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51) Table 56: A7-targeted amplification system A, and probes of A7-targeted amplification system A (one probe per PCR) Table 57: A7-targeted amplification system B, and probes of A7-targeted amplification system B (one probe per PCR) Table 58: A7-targeted amplification system C, and probes of A7-targeted amplification system C (one probe per PCR) Table 59: A7-targeted amplification system D, and probes of A7-targeted to amplification system D (one probe per PCR) Table 60: illustrative PCR material and method conditions, which can be used to test the specificity of the A9-targeted detection systems of the invention Tables 61-68: specificity results of A9-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51) Table 61: A9-targeted amplification system C, and probes of A9-targeted amplification system C (one probe per PCR) Table 62: A9-targeted amplification system E2, and probes of A9-targeted amplification system E2 (one probe per PCR) Table 63: A9-targeted amplification system E3, and probes of A9-targeted amplification system E3 (one probe per PCR) Table 64: A9-targeted amplification system E4, and probes of A9-targeted amplification system E4 (one probe per PCR) Table 65: A9-targeted amplification system F, and probes of A9-targeted amplification system F (one probe per PCR) Table 66: A9-targeted amplification system GZ7, and probes of A9-targeted amplification system GZ7 (one probe per PCR) Table 67: A9-targeted amplification system GZ8, and probes of A9-targeted amplification system GZ8 (one probe per PCR) Table 68: A9-targeted amplification system H, and probes of A9-targeted amplification system H (one probe per PCR)

The amplification and detection systems, which were used for the specificity tests, are those shown in Table 17 (A5-targeted systems); Table 23 (A6-targeted systems); Table 29 (A7-targeted systems); Table 35 (A9-targeted systems).

For the A9-targeted systems, those primers, which are shown between brackets in Table 35 were not used, as they would have been redundant: indeed, those primers, which are not between brackets, are sufficient to amplify all group A9 HPV. Hence, in table 35, those A9-targeted primers which are shown between brackets are optional and/or equivalent and/or alternative primers, if it is wished to amplify all group A9 HPV.

Tables 69-82: system sensitivity

The sensitivity of systems of the invention has been tested under the same experimental conditions, as for the specificity tests (see Tables 52, 55, 60).

Table 69: sensitivity of A5-targeted systems (systems A, B, C, D and E) Table 70: sensitivity of A6-targeted systems (systems A, B, C, D and E) Tables 71-74: sensitivity of A7-targeted systems Table 71: sensitivity of A7-targeted system A Table 72: sensitivity of A7-targeted system B Table 73: sensitivity of A7-targeted system C Table 74: sensitivity of A7-targeted system D Tables 75-82: sensitivity of A9-targeted systems Table 75: sensitivity of A9-targeted system C Table 76: sensitivity of A9-targeted system E2 Table 77: sensitivity of A9-targeted system E3 Table 78: sensitivity of A9-targeted system E4 Table 79: sensitivity of A9-targeted system F Table 80: sensitivity of A9-targeted system GZ7 Table 81: sensitivity of A9-targeted system GZ8 Table 82: sensitivity of A9-targeted system H Tables 83-88: “meqaplex” specificity and sensitivity

PCR runs have been conducted with one A5-targeted system, one A6-targeted system, one A7-targeted system, one A9-targeted system, in a single-tube amplification.

As the A7- and A9-targeted systems already are multiplex systems (i.e., they each have more than two primers), the mix of the four group-targeted systems is herein referred to as a “megaplex”.

The megaplex PCR have been tested with the plasmids listed in Table 51, in to specificity (Ct; RFU) and in sensitivity (Ct; RFU).

Tables 83-86: specificity results for megaplex EAAH and EBAC Tables 83-84: specificity of the megaplex EAAH Table 83: illustrative megaplex material and method conditions, which can be used for a mix of A5-targeted system E, A6-targeted system A, A7-targeted system A and A9-targeted system H (i.e., megaplex EAAH); these experimental conditions have been used for the results depicted in table 84 Table 84: specificity results of the EAAH megaplex Tables 85-86: specificity of the megaplex EBAC Table 85: illustrative megaplex material and method conditions, which can be used for a mix of A5-targeted system E, A6-targeted system B, A7-targeted system A and A9-targeted system C (i.e., megaplex EBAC); these experimental conditions have been used for the results depicted in table 86; Table 86: specificity results of the EBAC megaplex Tables 87-88: sensitivity results of the megaplex EAAH and EBAC Table 87: sensitivity results of the megaplex EAAH Table 88: sensitivity results of the megaplex EBAC Table 89: list of HPV genome sequences.

These tables are followed by a listing of sequences of reference templates.

A5 Group=HPV51; HPV26; HPV69; HPV82 A5 HR HPV=HPV51 A5 Reference Genome=HPV51 NC_(—)001533.1; Human HPV, Complete Genome

TABLE 12 A5 REFERENCE AMPLICON SEQUENCES (from reference genome) = Size Start and stop positions SEQ Systems (bp) within reference genome ID NO: System A 106 772-877 1 System AB 109 772-880 320 System AD 131 772-902 321 System B 145 736-880 2 System BA 142 736-877 322 System BD 167 736-902 323 System C 117 678-794 3 System CA 200 678-877 324 System CB 203 678-880 325 System CD 225 678-902 326 System CE 151 678-828 327 System D 192 711-902 4 System DA 167 711-877 328 System DB 170 711-880 329 System DE 118 711-828 330 System E 125 704-828 5 System EA 174 704-877 331 System EB 177 704-880 332 System ED 199 704-902 333

TABLE 13 A5 FORWARD PRIMERS Size SEQ Name Sequence Address (bp) ID NO: A5E6f1 GGCAGTGGAAAGCAGTGGAGAC 772 22 6 A5E6f2 AGCTCCGTGTTGCAGGTGTTC 736 21 7 A5E6f3 ATATGCGTGACCAGCTACCAG 678 21 8 A5E6f4 GACAGGCTACGTGTTACAGAA 711 21 9 A5E6f5 CGGGCTGGACAGGCTACG 704 18 10

TABLE 14 A5 REVERSE PRIMERS Size SEQ Name Sequence Address bp ID NO: A5E6r1 CCATCGCCGTTGCTAGTTGTTC 877 22 11 A5E6r2 AGTCCATCGCCGTTGCTAGTTG 880 22 12 A5E6r3 TGTCTCCACTGCTTTCCACTG 794 21 13 A5E6r4 CCCTCATCCTCTGTACCTTC 902 20 14 A5E6r5 TCGCCCATTAACATCTGCTGT 828 21 15

TABLE 15 A5 PROBES SEQ Corresponding Size ID beacon probes Sequence Address (bp) NO: A5E6s1, GCTTAGTTCGCCCATTAACA 835 27 16 A5E6s1b TCTGCTG A5E6s2 CGAAGGGTGTCTCCACTGCT 801 25 17 TTCCA A5E6s3 ACACGGAGCTTCAATTCTGT 745 26 18 AACACG A5E6s4 TAGTACAACTGGCAGTGGAA 762 26 19 AGCAGT

TABLE 16 A5 BEACON PROBES SEQ Sequence (underlined ID Name are shown the beacon arms) Address NO: A5E6s1 CCCCCTCGCTTAGTTCGCCCATTAACATCT 835 20 GCTGGAGGGGG A5E6s1b CGCTGCGCTTAGTTCGCCCATTAACATCTG 835 21 CTGGCAGCG A5E6s2 CGCGATCCGAAGGGTGTCTCCACTGCTTTC 801 22 CAGATCGCG A5E6s3 CGCGATCACACGGAGCTTCAATTCTGTAAC 745 23 ACGGATCGCG A5E6s4 CGCGATCTAGTACAACTGGCAGTGGAAAGC 762 24 AGTGATCGCG A5E6s4 CGCGATCTAGTACAACTGGCAGTGGAAAGC 762 24 AGTGATCGCG

TABLE 17 A5 systems; minimal set = one forward primer, one reverse primer, and one probe HPV51 reference amplicon Forward primer Reverse primer Probe Beacon ® Probe A5 SEQ ID NO: Name SEQ ID NO: Name SEQ ID NO: SEQ ID NO: Name SEQ ID NO: System A 1 A5E6f1 6 A5E6r1 11 16 A5E6s1 20 16 A5E6s1b 21 System AB 320 A5E6f1 6 A5E6r2 12 16 A5E6s1 20 16 A5E6s1b 21 System AD 321 A5E6f1 6 A5E6r4 14 16 A5E6s1 20 16 A5E6s1b 21 System B 2 A5E6f2 7 A5E6r2 12 17 A5E6s2 22 16 A5E6s1 20 16 A5E6s1b 21 System BA 322 A5E6f2 7 A5E6r1 11 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 System BD 323 A5E6f2 7 A5E6r4 14 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 System C 3 A5E6f3 8 A5E6r3 13 18 A5E6s3 23 System CA 324 A5E6f3 8 A5E6r1 11 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 18 A5E6s3 23 19 A5E6s4 24 System CB 325 A5E6f3 8 A5E6r2 12 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 18 A5E6s3 23 19 A5E6s4 24 System CD 326 A5E6f3 8 A5E6r4 14 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 18 A5E6s3 23 19 A5E6s4 24 System CE 327 A5E6f3 8 A5E6r5 15 18 A5E6s3 23 19 A5E6s4 24 System D 4 A5E6f4 9 A5E6r4 14 19 A5E6s4 24 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 System DA 328 A5E6f4 9 A5E6r1 11 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 19 A5E6s4 24 System DB 329 A5E6f4 9 A5E6r2 12 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 19 A5E6s4 24 System DE 330 A5E6f4 9 A5E6r5 15 19 A5E6s4 24 System D 4 A5E6f4 9 A5E6r4 14 19 A5E6s4 24 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 System DA 328 A5E6f4 9 A5E6r1 11 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 19 A5E6s4 24 System DB 329 A5E6f4 9 A5E6r2 12 16 A5E6s1 20 16 A5E6s1b 21 17 A5E6s2 22 19 A5E6s4 24 System DE 330 A5E6f4 9 A5E6r5 15 19 A5E6s4 24

A6 Group=HPV30; HPV63; HPV56; HPV66 A6 HR HPV=HPV56 A6 Reference Genome=HPV56 NC_(—)001594.1; Human HPV56, Complete Genome

TABLE 18 A6 REFERENCE AMPLICON SEQUENCES (from reference genome) = Size Start and stop positions SEQ Systems (bp) within reference genome ID NO: System A 100 504-603 25 System AE 288 504-791 334 System B 115 489-603 26 System BE 303 489-791 335 System C 138 413-550 27 System CA 191 413-603 336 System CE 379 413-791 337 System D 102 502-603 28 System DE 290 502-791 338 System E 127 665-791 29

TABLE 19 A6 FORWARD PRIMERS SEQ ID Name Sequence Address Size (bp) NO: A6E6f1 TGGACCGGGTCATGTTTGGG 504 20 30 A6E6f2 CTAATAGCACATGGTTGGACCG 489 22 31 A6E6f3 AAGGTGCTACAGATGTCAAAG 413 21 32 A6E6f4 GTTGGACCGGGTCATGTTTGG 502 21 33 A6E6f5 TCAGAGGATGAGGATGAGGATG 665 22 34

TABLE 20 A6 REVERSE PRIMERS SEQ ID Name Sequence Address Size bp NO: A6E6r1 ACGTCTTGCAGCGTTGGTAC 603 20 35 A6E6r1 ACGTCTTGCAGCGTTGGTAC 603 20 35 A6E6r2 GGTTCTCTAGATGTTTGTCT 550 22 36 CC A6E6r1 ACGTCTTGCAGCGTTGGTAC 603 20 35 A6E6r3 ACTGCACCACAAACTTACAC 791 22 37 TC

TABLE 21 A6 PROBES SEQ Corresponding Size ID beacon probes Sequence Address (bp) NO: A6E6s1 ACATCTAGAGAACCTAGAGA 537 30 38 ATCTACAGTA A6E6s2, GGTCCAACCATGTGCTATTA 509 26 39 A6E6s2b GATGAA A6E6s3, CGGCCACAGCAAGCTAGACA 707 20 40 A6E6s3b

TABLE 22 A6 BEACON PROBES SEQ Sequence (underlined ID Name are shown the beacon arms) Address NO: A6E6s1 CGCGATCACATCTAGAGAACCTAGAGAATC 537 41 TACAGTAGATCGCG A6E6s1 CGCGATCACATCTAGAGAACCTAGAGAATC 537 41 TACAGTAGATCGCG A6E6s2 CGCGATCGGTCCAACCATGTGCTATTAGAT 509 42 GAAGATCGCG A6E6s2b CGCCTCGGTCCAACCATGTGCTATTAGATG 509 43 AAGAGGCG A6E6s1 CGCGATCACATCTAGAGAACCTAGAGAATC 537 41 TACAGTAGATCGCG A6E6s3 CGCGACGGCCACAGCAAGCTAGACATCGCG 707 44 A6E6s3b CGCCTCCGGCCACAGCAAGCTAGACAGAGG 707 45 CG

TABLE 23 A6 SYSTEMS; minimal set = one forward primer, one reverse primer, and one probe HPV56 reference amplicon Forward primer Reverse Primer Probe Beacon ® Probe A6 SEQ ID NO: Name SEQ ID NO: Name SEQ ID NO: SEQ ID NO: Name SEQ ID NO: System A 25 A6E6f1 30 A6E6r1 35 38 A6E6s1 41 System 334 A6E6f1 30 A6E6r3 37 38 A6E6s1 41 AE 40 A6E6s3 44 40 A6E6s3b 45 System B 26 A6E6f2 31 A6E6r1 35 38 A6E6s1 41 System 335 A6E6f2 31 A6E6r3 37 38 A6E6s1 41 BE 40 A6E6s3 44 40 A6E6s3b 45 System C 27 A6E6f3 32 A6E6r2 36 39 A6E6s2 42 39 A6E6s2b 43 System 336 A6E6f3 32 A6E6r1 35 38 A6E6s1 41 CA 39 A6E6s2 42 39 A6E6s2b 43 System 337 A6E6f3 32 A6E6r3 37 38 A6E6s1 41 CE 39 A6E6s2 42 39 A6E6s2b 43 40 A6E6s3 44 40 A6E6s3b 45 System D 28 A6E6f4 33 A6E6r1 35 38 A6E6s1 41 System 338 A6E6f4 33 A6E6r3 37 38 A6E6s1 41 DE 40 A6E6s3 44 40 A6E6s3b 45 System E 29 A6E6f5 34 A6E6r3 37 40 A6E6s3 44 40 A6E6s3b 45

A7 Group=HPV18; HPV39; HPV45; HPV59; HPV68; HPV70; HPV85 A7 HR HPV=HPV18; HPV39; HPV45; HPV59; HPV68 A7 Reference Genome=HPV18 NC_(—)001357.1; Human HPV, Complete Genome

TABLE 24 A7 REFERENCE AMPLICON SEQUENCES (from reference genome) = Start and stop Size positions within SEQ ID Systems (bp) reference genome NO: Systems A, 198 à 209 1895-2099 46 A1, A2 1895-2102 47 1895-2103 48 1902-2099 49 1902-2102 50 1902-2103 51 System AB 161 à 171 1895-2062 52 1895-2065 53 1902-2062 339 1902-2065 340 Systems 199 a209 1895-2100 341 AC1, AC2, 1895-2103 48 AC3 1902-2100 342 1902-2103 51 System B 166 à 171 1895-2062 52 1895-2065 53 1896-2062 54 1896-2065 55 1897-2062 56 1897-2065 57 Systems 203 à 209 1895-2099 46 BA1, BA2, 1895-2102 47 BA3 1895-2103 48 1896-2099 343 1896-2102 344 1896-2103 345 1897-2099 346 1897-2102 347 1897-2103 348 Systems 204 à 209 1895-2100 349 BC1, BC2, 1895-2103 48 BC3 1896-2100 350 1896-2103 345 1897-2100 351 1897-2103 352 Systems 113 à 125 1987-2100 58 C, C1 1987-2103 59 1988-2100 60 1988-2103 61 1979-2100 62 1979-2103 63 Systems 112 à 125 1979-2099 353 CA1, CA2 1979-2102 354 1979-2103 63 1987-2099 355 1987-2102 356 1987-2103 59 1988-2099 357 1988-2102 358 1988-2103 61 System D 113 à 129  916-1032 64  916-1044 65  920-1032 66  920-1044 67

TABLE 25 A7 FORWARD PRIMERS SEQ Size ID Name Sequence Address (bp) NO: A7E16f1a TGGTATAGAACAGGAATATCAAAT 1895 24 68 A7E16f2a GAACAGGTATATCCAATATTAGTG 1902 24 69 A7E16f3a GAACAGGAATGTCCAATATTAG 1902 22 70 A7E115f1a TGGTATAGAACAGGAATATCAAAT 1895 26 71 AT A7E115f2a GTACAGAACAGGAATGTCCAA 1897 21 72 A7E115f3d GGTATCGCACAGGTATATCC 1896 20 73 A7E17f1 TGATAGCAATTTTGATTTGTCAG 1987 23 74 A7E17f2 GATAGCGTATTTGACCTATCAG 1988 22 75 A7E17f3 GGAATAGATGATAGTGTATTTGAT 1979 25 76 C A7E12f1 GGCCGATCCAGAAGGTACAGAC 916 22 77 A7E12f2 CAATCGTGAAGGTACAGATGG 920 21 78

TABLE 26 A7 REVERSE PRIMERS SEQ Size ID Name Sequence Address bp NO: A7E16r1b CATTGCTGTTGCAGTCTG 2099 18 79 A7E16r2b GCAGCATTACTGTTACAATC 2103 20 80 A7E16r3b CGGCGTTACTATTACTATCTG 2102 21 81 A7E115r1a TGCCATATCGCTTTCATCTG 2062 20 82 A7E115r2b AAATGCTATATCACTTTCATCTG 2065 23 83 A7E17r1 GCATTACTGTTGCTGTCTG 2100 19 84 A7E17r2 GCGGCATTACTATTACAATCTG 2103 22 85 A7E12r2 GCATTTTCATCCTCATCCTCTG 1032 22 86 A7E12r3 CCTGTGTCTGTTGCATTTTC 1044 20 87

TABLE 27 A7 PROBES Size SEQ ID Corresponding Sequence Address (bp) NO: beacon probes CAGATGAAAGCGATATGGCATT 2043 22 88 A7E1ZAS61f CAGATGAAAGTGATATTGCATAT 2043 23 89 A7E1ZAS63f CTGATGAAAGTGACATAGCATTT 2043 23 98 A7E1ZAS64f CAGATGAAAGTGATATGGCATTT 2043 23 91 A7E1ZCS40f TGGAATAGATGATAGTGTATTTGAT 1978 25 92 A7E1ZBS74f GATAGCAATTTTGATTTGTCAGA 1988 23 93 A7E1ZBS26f TGGAATAGATGATAGTGTATTTGAT 1978 25 92 A7E1ZBS74f AGTTGATGATAGCGTGTTTGAC 1981 22 94 A7E1ZBS79f AGTTGATGATAGCGTGTTTGAC 1981 22 94 A7E1ZBS80f CGATAGTAATTTTGATTTGTCAGA 1987 24 96 A7E1ZBS27f CAGATGAAAGTGATATGGCATTT 2043 23 91 A7E1ZCS11f CAGATGAAAGTGATATGGCATTT 2043 23 91 A7E1ZCS40f CTGATGAAAGTGACATAGCATTT 2043 23 90 A7E1ZCS45f CAGATGAAAGTGATATTGCATAT 2043 23 89 A7E1ZCS63f AATGAGTTAACAGATGAAAGTGA 2032 23 96 A7E1ZCS90f GTAATGGCTGGTTCTTYGTAGAAACAA 954 27 97 A7E1ZDS36f GTMCGGCTGGTTTTATGTACAAGCTA 954 27 98 A7E1ZDS37f GTAATGGATGGTTTTTTGTACAGGCAAT 954 28 99 A7E1ZDS38f GTAACGGATGGTTTTTTGTACAAGCAAT 954 28 100 A7E1ZDS2f GGTGTAATGGCTGGTTCITTGTAGA 951 25 101 A7E1ZDS3f GGTGTAATGGCTGGTTCTTTGTAGA 951 25 101 A7E1ZDS4f GGTGTAATGGCTGGTTCTTTGTAGA 951 25 101 A7E1ZDS11f

TABLE 28 A7 BEACON PROBES Sequence (underlined SEQ ID Name are shown the beacon arms) Address NO: A7E1ZAS61f CGACGTCAGATGAAAGCGATATGGCATTACGTCG 2043 102 A7E1ZAS63f CGACGTCAGATGAAAGTGATATTGCATATACGTCG 2043 103 A7E1ZAS64f CGACGTCTGATGAAAGTGACATAGCATTTACGTCG 2043 104 A7E1ZCS40f CCGAGTCAGATGMAGTGATATGGCATTTACTCGG 2043 106 A7E1ZBS74f ACGTCGTGGAATAGATGATAGTGTATTTGATCGACGT 1978 106 A7E1ZBS26f CGCAGTGATAGCAATTTTGATTTGTCAGAACTGCG 1988 107 A7E1ZBS74f ACGTCGTGGAATAGATGATAGTGTATTTGATCGACGT 1978 106 A7EIZBS79f ACGTCGAGTTGATGATAGCGTGTTTGACCGACGT 1981 108 A7E1ZBS80f CCGGCTAGTTGATGATAGCGTGTTTGACAGCCGG 1981 109 A7E1ZBS27f CGCAGTCGATAGTAATTTTGATTTGTCAGAACTGCG 1987 110 A7E1ZCS11f CGCAGTCAGATGAAAGTGATATGGCATTTACTGCG 2043 111 A7EIZCS40f CCGAGTCAGATGAAAGTGATATGGCATTTACTCGG 2043 105 A7E1ZCS45f CGTCGTCTGATGAAAGTGACATAGCATTTACGACG 2043 112 A7E1ZCS63f CGAGGTCAGATGAAAGTGATATTGCATATACCTCG 2043 113 A7EIZCS90f CCACGTAATGAGTTAACAGATGAAAGTGAACGTGG 2032 114 A7E1ZDS36f CGCGACGTAATGGCTGGTTCTTTGTAGAAACAAGTCGCG 954 115 A7E1ZDS37f CGCGATCGTAACGGCTGGTTTTATGTACAAGCTAGATCGCG 954 116 A7E1ZDS38f CGCGATCGTAATGGATGGTTTTTTGTACAGGCAATGATCGCG 954 117 A7E1ZDS2f CGCGCTGTAACGGATGGTTTTTTGTACAAGCAATAGCGCG 954 118 A7E1ZDS3f CGCGATGGTGTAATGGCTGGTTCTTTGTAGAATCGCG 951 119 A7E1ZDS4f CGCGATCGGTGTAATGGCTGGTTCTTTGTAGAGATCGCG 951 120 A7E1ZDS11f CTCGCTCGGTGTAATGGCTGGTTCTTTGTAGAGAGCGAG 951 121

TABLE 29 A7 SYSTEMS HPV18 reference amplicon Forward Primers Reverse Primers Probes Beacon ® Probes SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID A7 NO: Name NO: Name NO: NO: Name NO: System A 46 to 51 A7E16f1a 68 A7E16r1b 79 88 A7E1ZAS61f 102 A7E16f2a 69 A7E16r2b 80 89 A7E1ZAS63f 103 A7E16f3a 70 A7E16r3b 81 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 92 A7E1ZBS74f 106 System A1 46 to 51 A7E16f1a 68 A7E16r1b 79 93 A7E1ZBS26f 107 A7E16f2a 69 A7E16r2b 80 92 A7E1ZBS74f 106 A7E16f3a 70 A7E16r3b 81 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 95 A7E1ZBS27f 110 System A2 46 to 51 A7E16f1a 68 A7E16r1b 79 91 A7E1ZCS11f 111 A7E16f2a 69 A7E16r2b 80 91 A7E1ZCS40f 105 A7E16f3a 70 A7E16r3b 81 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System AB 52-53- A7E16f1a 68 A7E115r1a 82 93 A7E1ZBS26f 107 339-340 A7E16f2a 69 A7E115r2b 83 92 A7E1ZBS74f 106 A7E16f3a 70 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 95 A7E1ZBS27f 110 System AC1 48-51- A7E16f1a 68 A7E17r1 84 88 A7E1ZAS61f 102 341-342 A7E16f2a 69 A7E17r2 85 89 A7E1ZAS63f 103 A7E16f3a 70 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 92 A7E1ZBS74f 106 System AC2 48-51- A7E16f1a 68 A7E17r1 84 93 A7E1ZBS26f 107 341-342 A7E16f2a 69 A7E17r2 85 92 A7E1ZBS74f 106 A7E16f3a 70 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 95 A7E1ZBS27f 110 System AC3 48-51- A7E16f1a 68 A7E17r1 84 91 A7E1ZCS11f 111 341-342 A7E16f2a 69 A7E17r2 85 91 A7E1ZCS40f 105 A7E16f3a 70 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System B 52 to −57 A7E115f1a 71 A7E115r1a 82 93 A7E1ZBS26f 107 A7E115f2a 72 A7E115r2b 83 92 A7E1ZBS74f 106 A7E115f3d 73 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 95 A7E1ZBS27f 110 System BA1 46-47-48- A7E115f1a 71 A7E16r1b 79 88 A7E1ZAS61f 102 343 to A7E115f2a 72 A7E16r2b 80 89 A7E1ZAS63f 103 348 A7E115f3d 73 A7E16r3b 81 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 92 A7E1ZBS74f 106 System BA2 46-47-48- A7E115f1a 71 A7E16r1b 79 93 A7E1ZBS26f 107 343 to A7E115f2a 72 A7E16r2b 80 92 A7E1ZBS74f 106 348 A7E115f3d 73 A7E16r3b 81 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 96 A7E1ZBS27f 110 System BA3 46-47-48- A7E115f1a 71 A7E16r1b 79 91 A7E1ZCS11f 111 343 to A7E115f2a 72 A7E16r2b 80 91 A7E1ZCS40f 105 348 A7E115f3d 73 A7E16r3b 81 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System BC1 48-345- A7E115f1a 71 A7E17r1 84 88 A7E1ZAS61f 102 349 to A7E115f2a 72 A7E17r2 85 89 A7E1ZAS63f 103 352 A7E115f3d 73 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 92 A7E1ZBS74f 106 System BC2 48-345- A7E115f1a 71 A7E17r1 84 93 A7E1ZBS26f 107 349 to A7E115f2a 72 A7E17r2 85 92 A7E1ZBS74f 106 352 A7E115f3d 73 94 A7E1ZBS79f 108 94 A7E1ZBS80f 109 95 A7E1ZBS27f 110 System BC3 48-345- A7E115f1a 71 A7E17r1 84 91 A7E1ZCS11f 111 349 to A7E115f2a 72 A7E17r2 85 91 A7E1ZCS40f 105 352 A7E115f3d 73 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System C 58 to 63 A7E17f1 74 A7E17r1 84 91 A7E1ZCS11f 111 A7E17f2 75 A7E17f2 85 91 A7E1ZCS40f 105 A7E17f3 76 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System C1 58 to 63 A7E17f1 74 A7E17r1 84 88 A7E1ZAS61f 102 A7E17f2 75 A7E17r2 85 89 A7E1ZAS63f 103 A7E17f3 76 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 96 A7E1ZCS90f 114 System CA1 59-61-63- A7E17f1 74 A7E16r1b 74 91 A7E1ZCS11f 111 353 to A7E17f2 75 A7E16r2b 80 91 A7E1ZCS40f 105 358 A7E17f3 76 A7E16r3b 81 90 A7E1ZCS45f 112 89 A7E1ZCS63f 113 96 A7E1ZCS90f 114 System CA2 59-61-63- A7E17f1 74 A7E16r1b 79 88 A7E1ZAS61f 102 353 to A7E17f2 75 A7E16r2b 80 89 A7E1ZAS63f 103 358 A7E17f3 76 A7E16r3b 81 90 A7E1ZAS64f 104 91 A7E1ZCS40f 105 96 A7E1ZCS90f 114 System D 64 to 67 A7E12f1 77 A7E12r2 86 97 A7E1ZDS36f 115 A7E12f2 78 A7E12r3 87 98 A7E1ZDS37f 116 99 A7E1ZDS38f 117 100 A7E1ZDS2f 118 101 A7E1ZDS3f 119 101 A7E1ZDS4f 120 101 A7E1ZDS11f 121

A9 Group=HPV16; HPV31; HPV33; HPV35; HPV52; HPV58; HPV67 A9 HR HPV=HPV16; HPV31; HPV33; HPV35; HPV52; HPV58 A9 Reference Genome=HPV16 NC_(—)001526.1; Human HPV16, Complete Genome

TABLE 30 A9 REFERENCE AMPLICON SEQUENCES (from reference genome) = Amplicons Forward Reverse Start-stop Systems size bp address address positions SEQ ID NO: System C 88 2707 2794 2707-2794 122 2707 2794 2707 2707 2707 2707 2707 System E1 191 à 198 3600 3790 3600-3790 123 3600 3793 3600-3793 124 3600 3791 3600-3791 125 3790 3600-3797 126 3797 3600-3795 127 3795 System E2 190 à 198 3600 3790 3600-3790 123 3601 3793 3600-3793 124 3600 3791 3600-3791 125 3790 3600-3797 126 3797 3600-3795 127 3795 3601-3790 128 3601-3793 129 3601-3791 130 3601-3797 131 3601-3795 132 Amplicons address address Start-stop Systems size pb forw rev position SEQ ID NO: System E3 188 à 193 3600 3788 3600-3788 133 3601 3792 3600-3792 134 3600 3792 3600-3790 135 3790 3601-3788 136 3792 3601-3792 137 3792 3601-3790 138 3792 3790 System E4 179 à 186 3607 3788 3607-3788 139 3610 3792 3607-3792 140 3609 3792 3607-3790 141 3790 3610-3788 142 3792 3610-3792 143 3792 3610-3790 144 3792 3609-3788 145 3790 3609-3792 146 3609-3790 147 System E5 181 à 191 3607 3790 3607-3790 141 3610 3793 3607-3791 359 3609 3791 3607-3793 360 3790 3607-3795 361 3797 3607-3797 362 3795 3609-3790 363 3609-3791 364 3609-3793 365 3609-3795 366 3609-3797 367 3610-3790 144 3610-3791 368 3610-3793 369 3610-3795 370 3610-3797 371 System E6 189 à 193 3600 3788 3600-3788 133 3600 3792 3600-3790 135 3600 3792 3600-3792 134 3790 3792 3792 3792 3790 System E1H 231 à 241 3600 3838 3600-3830 372 Z7, Z8 3600 3831 3600-3831 373 3600 3830 3600-3837 374 3830 3600-3838 375 3838 3600-3839 376 3840 3600-3840 377 3839 3838 3837 System E2H 230 à 241 3600 3838 3600-3830 372 Z7, Z8 3601 3831 3600-3831 373 3600 3830 3600-3837 374 3830 3600-3838 375 3838 3600-3839 376 3840 3600-3840 377 3839 3601-3830 378 3838 3601-3831 379 3837 3601-3837 380 3601-3838 381 3601-3839 382 3601-3840 383 System E4H 224 à 234 3607 3838 3607-3830 384 Z7, Z8 3610 3831 3607-3831 385 3609 3830 3607-3837 386 3830 3607-3838 387 3838 3607-3839 388 3840 3607-3840 389 3839 3609-3830 390 3838 3609-3831 391 3837 3609-3837 392 3609-3838 393 3609-3839 394 3609-3840 395 3610-3830 396 3610-3831 397 3610-3837 398 3610-3838 399 3610-3839 400 3610-3840 401 System F 163 à 172 3626 3788 3626-3788 148 3626 3792 3626-3792 149 3621 3792 3626-3790 150 3625 3790 3621-3788 151 3792 3621-3792 152 3792 3621-3790 153 3792 3625-3788 154 3790 3625-3792 155 3625-3790 156 System FE 165 à 177 3626 3790 3621-3790 153 3626 3793 3621-3791 402 3621 3791 3621-3793 403 3625 3790 3621-3795 404 3797 3621-3797 405 3795 3625-3790 156 3625-3791 406 3625-3793 407 3625-3795 408 3625-3797 409 3626-3790 150 3626-3791 410 3626-3793 411 3626-3795 412 3626-3797 413 System FH 205 à 220 3626 3838 3621-3830 163 Z7, Z8 3626 3831 3621-3831 162 3621 3830 3621-3837 164 3625 3830 3621-3838 414 3838 3621-3839 415 3840 3621-3840 161 3839 3625-3830 167 3838 3625-3831 166 3837 3625-3837 168 3625-3838 416 3625-3839 417 3625-3840 165 3626-3830 159 3626-3831 158 3626-3837 160 3626-3838 418 3626-3839 419 3626-3840 157 System G Z7, 205 à 220 3626 3840 3626-3840 157 Z8 3626 3831 3626-3831 158 3621 3830 3626-3830 159 3625 3837 3626-3837 160 3840 3621-3840 161 3840 3621-3831 162 3621-3830 163 3621-3837 164 3625-3840 165 3625-3831 166 3625-3830 167 3625-3837 168 System H 132 à 150 3699 3838 3699-3838 169 3691 3831 3699-3831 170 3693 3830 3699-3830 171 3696 3830 3699-3840 172 3695 3838 3699-3839 173 3698 3840 3699-3837 174 3697 3839 3691-3838 175 3699 3838 3691-3831 176 3698 3837 3691-3830 177 3691-3840 178 3691-3839 179 3691-3837 180 3693-3838 181 3693-3831 182 3693-3830 183 3693-3840 184 3693-3839 185 3693-3837 186 System H 132 à 150 3696 3838 3696-3838 187 3695 3831 3696-3831 188 3698 3830 3696-3830 189 3697 3840 3696-3840 190 3839 3696-3839 191 3837 3696-3837 192 3695-3838 193 3695-3831 194 3695-3830 195 3695-3840 196 3695-3839 197 3695-3837 198 3698-3838 199 3698-3831 200 3698-3830 201 3698-3840 202 3698-3839 203 3698-3837 204 3697-3838 205 3697-3831 206 3697-3830 207 3697-3840 208 3697-3839 209 3697-3837 210

TABLE 31 A9 FORWARD PRIMERS Forward Primer SEQ ID Name 5′ Sequence 3′ address size bp NO: A9E1f7 AGGACGTGGTCCAGATTAAGTTT 2707 23 211 A9E118 AGGACGTGGTGCAGATTAAG 2707 20 212 A9E1f9 AGGACGTGGTGCAAATTAAGTTT 2707 23 213 A9E1f10 AGGACGTGGTGCAGATTAAATTT 2707 23 214 A9E1f11 AGGACGTGGTGCAGATTAGGTTT 2707 23 215 A9E1f12 AGGACGTGGTGCAAATTAAATTT 2707 23 216 A9E1f13 AGGACGTGGTGCAAATTAGGTTT 2707 23 217 A9E2f1 TAGTAACACTACACCCATAGTACAT 3600 25 218 A9E2f2 TCTAACGTTGCACCTATCGTG 3600 21 219 A9E2f4 TCCTTCTACTGCACCTATAATACA 3600 24 220 A9E2f1a TAGTACCACTACACCCATAGTACAT 3600 26 221 A9E2f2a TCTAACGTTGCACCTATCGTGCAT 3601 24 222 A9E2f4a TCCTTCTACTGCACCTATAATACAC 3600 25 223 A9E2Z5Z6f1c ACTACACCTATAGTACATTTAAAAGG 3607 26 224 A9E2Z5Z6f2c GCACCTATAGTGCATTTAAAAG 3610 22 225 A9E2Z5Z6f3b TGCACCTATAATACACCTAAAAG 3609 23 226 A9E21f1az TAAAAGGTGATGCTAATACTTTAAA 3626 25 227 A9E21f2bz TAAAAGGTGATGCAAATACATTAAA 3626 25 228 A9E21f3dz GCATTTAAAAGGTGAATCAAATAG 3621 24 229 A9E21f4cz CTAAAAGGTGATCCTAATAGTTTAAA 3625 26 230 A9E2f5 GTCGTCTACATGGCATTGGA 3699 20 231 A9E2f6 CAAGATGCTTCATCTACATGGAG 3691 23 232 A9E2f7 AGAAGCGTCATCTACATGGAG 3693 21 233 A9E2f8 AGTGTCGTCTACATGGCATTG 3696 21 234 A9E2f9 ATATGTCATCTACATGGCATTGG 3695 23 235 A9E2f10 TGTCATCCAGATGGCATTGG 3698 20 236 A9E2f10b ATGTCATCCACATGGCATTG 3697 20 237 A9E2f11 TTCATCTACCTGGAGTTGGAC 3699 21 238 A9E2f12 TTTCATCTACATGGAGTTGGAC 3698 22 239

TABLE 32 A9 REVERSE PRIMERS SEQ Reverse Primer size ID Name 5′ Sequence 3′ address bp NO: A9E1r5 TGTCCTGACACACATTTAAACG 2794 22 240 A9E1r6 TGTCCTGCACTGCATTTAAAC 2794 21 241 A9E2r1 ATTGGTCACGTTGCCATTG 3790 19 242 A9E2r2 AAAATTGTTGACGTTGTGTTTC 3793 22 243 A9E2r3 AACTGTTGACGTTGTGTTTC 3791 20 244 A9E2r4 ACATTTGTCGTTGCGGTTC 3790 19 245 A9E2r13 GTCTCTTTGTGATGTACTTATATA 3797 26 246 TG A9E2r14 CCCTTTGATATTCTGTTGTGTAAG 3795 24 247 A9E21r1cz TGGTCACGTTGCCATTC 3788 17 248 A9E21r2az AAAATCGTGTCTTTGTGATGT 3792 21 249 A9E21r3az AAACATTTGTTGTTGCTGTTC 3792 21 250 A9E21r4fz ATTTATCCCTTTGATATTCTGTTG 3790 24 251 A9E21r5az AAACAGTTGACGTTGTGTTTC 3792 21 252 A9E21r6az AAACTGTTGACGTTGTGTTTC 3792 21 253 A9E21r7az AAATTGTTGACGTTGTGTTTC 3792 21 254 A9E21r8az ACAGTTGTCGTTGTGTTTC 3790 19 255 A9E2r7C AAATCCTGTAGACACTGTAACAGT 3840 24 256 A9E2r8 ACTTATTTGCACAGTAGGTGGT 3831 22 257 A9E2r10 CTTACTTGCACAGTAGTTGGTA 3830 22 258 A9E2r12 ATCCTGTTGACACTGATACTGT 3837 22 259 A9E2r12B TATCCTGTAGACACTGAAACTGTG 3840 24 260 A9E2r15 AAATCCAGTAGACACTGTAATAGT 3840 25 261 T A9E2r7B ATCCTGTAGACACTGTAACAGTT 3838 23 262 A9E2r8 ACTTATTTGCACAGTAGGTGGT 3831 22 257 A9E2r9 CTTACTTGCACAGTAGGTGGTA 3830 22 263 A9E2r10 CTTACTTGCACAGTAGTTGGTA 3830 22 258 A9E2r12 ATCCTGTTGACACTGATACTGT 3838 22 259 A9E2r7C AAATCCTGTAGACACTGTAACAGT 3840 24 256 A9E2r12B TATCCTGTAGACACTGAAACTGTG 3839 24 264 A9E2r15 AAATCCAGTAGACACTGTAATAGT 3838 26 261 TT A9E2r16 ACCGTACTTATTTGCACAGTG 3837 21 265

TABLE 33 A9 PROBES 5′ Sequence 3′ address size pb SEQ ID NO: Corresponding beacon probes TCCATCGTTTTCCTTGTCCTCT 2738 22 266 A9E1S10 and S10a TCCATCGTTTTCTTTGACCTCT 2738 22 267 A9E1S11 and S11a TCCATCATTTTCTTTGACCTCT 2738 22 268 A9E1S12, S12a and S12b TCTCCATCATTTTCTTTGTCCTCT 2738 24 269 A9E1S13a, S13b and S13c CTCCATCGTTTTCTTTGTCCTC 2739 22 270 A9E1S14a CTCCATCATTTTCTTTGACCTCTC 2737 24 271 A9E1S15a and 15b AGTGTCGTCTACATGGCATTGGAC 3696 24 272 A9E2Z7S1 ATATGTCATCCACCTGGCATTGGAC 3695 25 273 A9E2Z7S2 and S2a ATATGTCATCCACCTGGCATTGGA 3695 24 274 A9E2Z7S2b ATGCTTCATCTACATGGAGATGGAC 3695 25 275 A9E2Z7S3 and S3a CAAGTTTCATCTACATGGCATTGGAC 3694 26 276 A9E2Z7S4 and S4a GATAGTGAATGGCAACGTGA 3766 20 277 A9E2Z8S2f, S21f and S28f ATAAGTACATCACAAAGAGACGA 3766 23 278 A9E2Z8S56f, S58f and S61f TAACTGAACAGCAACAACAAATG 3767 23 279 A9E2Z8S101f, 105f and 127f CACAACAGAATATCAAAGGGATAAATT 3765 27 280 A9E2Z8S146f, 155f and 156f CGTACAGTGATGAAACACAAC 3761 21 281 A9E2Z8S210f AACGGAAACACAACGACAAC 3768 20 282 A9E2Z8S231f, 236f and 250f

TABLE 34 A9 BEACON PROBES Beacon probe Name 5′ Sequence 3′ address size bp SEQ ID NO: A9E1S10 CGCGATTCCATCGTTTTCCTTGTCCTCTATCGCG 2738 22 283 A9E1S10a CGCGATCCATCGTTTTCCTTGTCCTCTTCGCG 2738 22 284 A9E1S11 CGCGATTCCATCGTTTTCTTTGACCTCTATCGCG 2738 22 285 A9E1S11a CGCGATCCATCGTTTTCTTTGACCTCTTCGCG 2738 22 286 A9E1S12 CGCGATTCCATCATTTTCTTTGACCTCTATCGCG 2738 22 287 A9E1S12a CGCGATCCATCATTTTCTTTGACCTCTTCGCG 2738 22 288 A9E1S12b CGCTGTCCATCATTTTCTTTGACCTCTCAGCG 2738 22 289 A9E1S13a CGCGTTCTCCATCATTTTCTTTGTCCTCTACGCG 2738 24 290 A9E1S13b CGCCGTCTCCATCATTTTCTTTGTCCTCTCGGCG 2738 24 291 A9E1S13c CGCGATTCTCCATCATTTTCTTTGTCCTCTATCGCG 2738 24 292 A9E1S14a CGCGATCTCCATCGTTTTCTTTGTCCTCATCGCG 2739 22 293 A9E1S15a CGCCGCTCCATCATTTTCTTTGACCTCTCCGGCG 2737 24 294 A9E1S15b CGCGATCTCCATCATTTTCTTTGACCTCTCATCGCG 2737 24 295 A9E2Z7S1 CGCGAAGTGTCGTCTACATGGCATTGGACTCGCG 3696 24 296 A9E2Z7S2 CGCTCGATATGTCATCCACCTGGCATTGGACCGAGCG 3695 25 297 A9E2Z7S2a CGCATGATATGTCATCCACCTGGCATTGGACCATGCG 3695 25 298 A9E2Z7S2b CGCATGATATGTCATCCACCTGGCATTGGACATGCG 3695 24 299 A9E2Z7S3 CGCACTATGCTTCATCTACATGGAGATGGACAGTGCG 3695 25 300 A9E2Z7S3a CCGACGATGCTTCATCTACATGGAGATGGACCGTCGG 3695 25 301 A9E2Z7S4 CGCGATCAAGTTTCATCTACATGGCATTGGACATCGCG 3694 26 302 A9E2Z7S4a CGCGAGCAAGTTTCATCTACATGGCATTGGACCTCGCG 3694 26 303 A9E2Z8S2f CAGCGTGATAGTGAATGGCAACGTGAACGCTG 3766 20 304 A9E2Z8S21f CGGACTGATAGTGAATGGCAACGTGAAGTCCG 3766 20 305 A9E2Z8S28f CTCGCTGATAGTGAATGGCAACGTGAAGCGAG 3766 20 306 A9E2Z8S56f CGAGCTATAAGTACATCACAAAGAGACGAAGCTCG 3766 23 307 A9E2Z8S58f CGCAGTATAAGTACATCACAAAGAGACGAACTGCG 3766 23 308 A9E2Z8S61f CGCGTTATAAGTACATCACAAAGAGACGAAACGCG 3766 23 309 A9E2Z8S101f CGAGGTTAACTGAACAGCAACAACAAATGACCTCG 3767 23 310 A9E2Z8S105f CGCGATTAACTGAACAGCAACAACAAATGATCGCG 3767 23 311 A9E2Z8S127f CCGGCTTAACTGAACAGCAACAACAAATGAGCCGG 3767 23 312 A9E2Z8S146f CGCGATCACAACAGAATATCAAAGGGATAAATTATCGCG 3765 27 313 A9E2Z8S155f CGCACGCACAACAGAATATCAAAGGGATAAATTCGTGCG 3765 27 314 A9E2Z8S156f CCGGCTCACAACAGAATATCAAAGGGATAAATTAGCCGG 3765 27 315 A9E2Z8S210f CCGGCTCGTACAGTGATGAAACACAACAGCCGG 3761 21 316 A9E2Z8S231f CGAGGTAACGGAAACACAACGACAACACCTCG 3768 20 317 A9E2Z8S236f CGCGTTAACGGAAACACAACGACAACAACGCG 3768 20 318 A9E2Z8S250f CGATGCAACGGAAACACAACGACAACGCATCG 3768 20 319

TABLE 35 A9 SYSTEMS HPV16 reference Forward Primer Reverse Primer Beacon ® Probe amplicon SEQ SEQ Probe SEQ A9 SEQ ID NO: Name ID NO: Name ID NO: SEQ ID NO: Name ID NO: System C 122 A9E1f8 212; 214; A9E1r5 240-241 266-271 A9E1S10 283-295 A9E1f10 216 A9E1r6 A9E1S10a A9E1f12 (211; 213; — (A9E1f7) 215; 217) A9E1S11 (A9E1f9) A9E1S11a (A9E1f11) — (A9E1f13) A9E1S12 A9E1S12a A9E1S12b — A9E1S13a A9E1S13b A9E1S13c — A9E1S14a — A9E1S15a A9E1S15b System E1 123 to 127 A9E2f1 218-220 A9E2r1 242-243; 272-276 A9E2Z7S1 296-303 A9E2f2 A9E2r2 245-247 — A9E2f4 A9E2r4 (244) A9E2Z7S2 A9E2r13 A9E2Z7S2a A9E2r14 A9E2Z7S2b (A9E2r3) — A9E2Z7S3 A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System E2 123 to 132 A9E2f1a 221-223 A9E2r1 242-243; 272-276 A9E2Z7S1 296-303 A9E2f2a A9E2r2 245-247 — A9E2f4a A9E2r4 (244) A9E2Z7S2 A9E2r13 A9E2Z7S2a A9E2r14 A9E2Z7S2b (A9E2r3) — A9E2Z7S3 A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System E3 133 to 138 A9E2f1a 221-223 A9E21r1cz 248-252 272-276 A9E2Z7S1 296-303 A9E2f2a A9E21r2az (253-255) — A9E2f4a A9E21r3az A9E2Z7S2 A9E21r4fz A9E2Z7S2a A9E21r5az A9E2Z7S2b (A9E21r6az) — (A9E21r7az) A9E2Z7S3 (A9E21r8az) A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System E4 139 to 147 A9E2Z5Z6f1c 224-226 A9E21r1cz 248-252 272-276 A9E2Z7S1 296-303 A9E2Z5Z6f2c A9E21r2az (253-255) — A9E2Z5Z6f3b A9E21r3az A9E2Z7S2 A9E21r4fz A9E2Z7S2a A9E21r5az A9E2Z7S2b (A9E21r6az — A9E21r7az A9E2Z7S3 A9E21r8az) A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System E5 141; 144 and 359 A9E2Z5Z6f1c 224-226 A9E2r1 242-243; 272-276 A9E2Z7S1 296-303 to 371 A9E2Z5Z6f2c A9E2r2 245-247; — A9E2Z5Z6f3b A9E2r4 (244) A9E2Z7S2 A9E2r13 A9E2Z7S2a A9E2r14 A9E2Z7S2b (A9E2r3) — A9E2Z7S3 A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System E6 133 to 135 A9E2f1 218-220 A9E21r1cz 248-252; 272-276 A9E2Z7S1 296-303 A9E2f2 A9E21r2az (253-255) — A9E2f4 A9E21r3az A9E2Z7S2 A9E21r4fz A9E2Z7S2a A9E21r5az A9E2Z7S2b (A9E21r6az) — (A9E21r7az) A9E2Z7S3 (A9E21r8az) A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System 372 to 377 A9E2f1 218-220 (A9E2r7B) (256; 257; 259; 262; 263); 272-276 A9E2Z7S1 296-303 E1H Z7 A9E2f2 (A9E2r8) 258; 261; 264; 265 — A9E2f4 (A9E2r9) A9E2Z7S2 A9E2r10 A9E2Z7S2a (A9E2r12) A9E2Z7S2b (A9E2r7C) — A9E2r12B A9E2Z7S3 A9E2r15 A9E2Z7S3a A9E2r16 — A9E2Z7S4 A9E2Z7S4a System 372 to 377 A9E2f1 218-220 (A9E2r7B) (256; 257; 259, 277-282 A9E2Z8S2f 304-319 E1H Z8 A9E2f2 (A9E2r8) 262; 263); A9E2Z8S21f A9E2f4 (A9E2r9) 258; 261; 264; A9E2Z8S28f A9E2r10 265 — (A9E2r12) A9E2Z8S56f (A9E2r7C) A9E2Z8S58f A9E2r12B A9E2Z8S61f A9E2r15 — A9E2r16 A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f System 372 to 383 A9E2f1a 221-223 (A9E2r7B) (256; 257; 259, 262; 263); 272-276 A9E2Z7S1 296-303 E2H Z7 A9E2f2a (A9E2r8) 258; 261; 264; 265 — A9E2f4a (A9E2r9) A9E2Z7S2 A9E2r10 A9E2Z7S2a (A9E2r12) A9E2Z7S2b (A9E2r7C) — A9E2r12B A9E2Z7S3 A9E2r15 A9E2Z7S3a A9E2r16 — A9E2Z7S4 A9E2Z7S4a System 372 to 383 A9E2f1a 221-223 (A9E2r7B) (256; 257; 259; 262; 263); 277-282 A9E2Z8S2f 304-319 E2H Z8 A9E2f2a (A9E2r8) 258; 261; 264; 265 A9E2Z8S21f A9E2f4a (A9E2r9) A9E2Z8S28f A9E2r10 — (A9E2r12) A9E2Z8S56f (A9E2r7C) A9E2Z8S58f A9E2r12B A9E2Z8S61f A9E2r15 — A9E2r16 A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f System 384 to 401 A9E2Z5Z6f1c 224-226 (A9E2r7B) (256; 257; 259; 272-276 A9E2Z7S1 296-303 E4H Z7 A9E2Z5Z6f2c (A9E2r8) 262; 263); — A9E2Z5Z6f3b (A9E2r9) 258; 261; 264; A9E2Z7S2 A9E2r10 265 A9E2Z7S2a (A9E2r12) A9E2Z7S2b (A9E2r7C) — A9E2r12B A9E2Z7S3 A9E2r15 A9E2Z7S3a A9E2r16 — A9E2Z7S4 A9E2Z7S4a System 384 to 401 A9E2Z5Z6f1c 224-226 (A9E2r7B) (256; 257; 259; 262; 263); 277-282 A9E2Z8S2f 304-319 E4H Z8 A9E2Z5Z6f2c (A9E2r8) 258; 261; 264; 265 A9E2Z8S21f A9E2Z5Z6f3b (A9E2r9) A9E2Z8S28f A9E2r10 — (A9E2r12) A9E2Z8S56f (A9E2r7C) A9E2Z8S58f A9E2r12B A9E2Z8S61f A9E2r15 — A9E2r16 A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f System F 148 to 156 A9E21f1az 227-230 A9E21r1cz 248-252; 272-276 A9E2Z7S1 296-303 A9E21f2bz A9E21r2az (253-255) — A9E21f3dz A9E21r3az A9E2Z7S2 A9E21f4cz A9E21r4fz A9E2Z7S2a A9E21r5az A9E2Z7S2b (A9E21r6az) — (A9E21r7az) A9E2Z7S3 (A9E21r8az) A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System FE 150; 153; 156; 402 to A9E21f1az 227-230 A9E2r1 242-243; 272-276 A9E2Z7S1 296-303 413 A9E21f2bz A9E2r2 (244); — A9E21f3dz (A9E2r3) 245-247 A9E2Z7S2 A9E21f4cz A9E2r4 A9E2Z7S2a A9E2r13 A9E2Z7S2b A9E2r14 — A9E2Z7S3 A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System FH 157 to 168 and 414 A9E21f1az 227-230 (A9E2r7B) (262); 272-276 A9E2Z7S1 296-303 Z7 to 419 A9E21f2bz (A9E2r8) (257); — A9E21f3dz (A9E2r9) (263); A9E2Z7S2 A9E21f4cz (A9E2r12) (259); A9E2Z7S2a (A9E2r7C) (256); A9E2Z7S2b A9E2r10 258; — A9E2r12B 264 A9E2Z7S3 A9E2r15 261 A9E2Z7S3a A9E2r16 265 — A9E2Z7S4 A9E2Z7S4a System FH 157 to 168 and 414 A9E21f1az 227-230 (A9E2r7B) (262); 277-282 A9E2Z8S2f 304-319 Z8 to 419 A9E21f2bz (A9E2r8) (257); A9E2Z8S21f A9E21f3dz (A9E2r9) (263); A9E2Z8S28f A9E21f4cz (A9E2r12) (259); — (A9E2r7C) (256); A9E2Z8S56f A9E2r10 258; A9E2Z8S58f A9E2r12B 264 A9E2Z8S61f A9E2r15 261 — A9E2r16 265 A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f System G 157 to 168 A9E21f1az 227-230 (A9E2r7C) (256); 272-276 A9E2Z7S1 296-303 Z7 A9E21f2bz A9E2r8 257-261 — A9E21f3dz A9E2r10 A9E2Z7S2 A9E21f4cz A9E2r12 A9E2Z7S2a A9E2r12B A9E2Z7S2b A9E2r15 — A9E2Z7S3 A9E2Z7S3a — A9E2Z7S4 A9E2Z7S4a System G 157 to 168 A9E21f1az 227-230 (A9E2r7C) (256); 277-282 A9E2Z8S2f 304-319 Z8 A9E21f2bz A9E2r8 257-261 A9E2Z8S21f A9E21f3dz A9E2r10 A9E2Z8S28f A9E21f4cz A9E2r12 — A9E2r12B A9E2Z8S56f A9E2r15 A9E2Z8S58f A9E2Z8S61f — A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f System H 169 to 210 (A9E2f5) (231); (A9E2r7B) (262); 277-282 A9E2Z8S2f 304-319 A9E2f6 232; (A9E2r8) (257); A9E2Z8S21f (A9E2f7) (233); (A9E2r9) (263); A9E2Z8S28f A9E2f8 234; (A9E2r12) (259); — A9E2f9 235; (A9E2r7C) (256); A9E2Z8S56f (A9E2f10) (236); A9E2r10 258; A9E2Z8S58f (A9E2f10b) (237); A9E2r12B 264; A9E2Z8S61f (A9E2f11) (238); A9E2r15 261; — (A9E2f12) (239) A9E2r16 265 A9E2Z8S101f A9E2Z8S105f A9E2Z8S127f — A9E2Z8S146f A9E2Z8S155f A9E2Z8S156f — A9E2Z8S210f — A9E2Z8S231f A9E2Z8S236f A9E2Z8S250f Those primers which are between brackets are optional and/or equivalent and/or alternative primers.

TABLE 36 A5 Systems A to C: sequence aligment mismach evaluation Reference of sequence: HPV 56->ref|NC_001594.1| System A System B System C forward reverse forward reverse forward reverse primer primer probe primer primer probe primer primer SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 6 NO: 11 NO: 20 NO: 7 NO: 12 NO: 22 NO: 8 NO: 13 NO: 23 N^(o)HPC Group A5E6f1 A5E6r1 A5E6s1 A5E6f2 A5E6r2 A5E6s2 A5E6f3 A5E6r3 A5E6s3 51 A5 0 0 0 0 0 0 0 0 0 26 A5 7 11 8 7 8 7 5 6 4 69 A5 8 9 8 10 7 9 6 7 6 82 A5 1 4 3 4 4 1 3 0 5 56 A6 12 13 10 9 12 12 10 13 8 30 A6 12 10 8 6 10 15 11 13 8 53 A6 12 11 11 6 11 15 9 13 6 66 A6 12 14 10 8 13 13 10 13 8 18 A7 7 18 11 9 18 7 18 7 13 39 A7 10 16 7 8 16 11 18 10 11 45 A7 9 16 11 10 17 10 19 8 13 59 A7 9 17 7 9 16 12 18 9 12 68 A7 12 16 10 8 16 12 16 11 10 85 A7 9 17 9 11 16 10 17 9 14 70 A7 11 17 11 9 16 11 16 10 12 16 A9 12 13 9 8 14 12 16 12 12 16 A9 12 13 9 8 14 13 16 12 12 31 A9 12 13 9 11 14 13 16 12 14 33 A9 14 15 11 11 15 13 17 13 13 35 A9 14 14 12 9 15 15 16 14 12 52 A9 14 16 10 11 15 11 17 13 13 58 A9 14 14 9 9 14 14 17 14 12 67 A9 13 15 8 10 15 13 17 13 12 54 A 14 12 14 12 12 15 21 13 42 A1 13 10 10 11 10 15 19 13 13 32 A1 13 11 9 13 11 15 18 13 13 61 A3 11 19 13 9 20 14 18 12 13 72 A3 9 20 14 7 20 13 21 10 14 89 A3 16 18 12 8 18 19 21 16 13 86 A3 12 18 11 11 19 14 21 13 16 87 A3 13 18 12 11 19 15 21 14 16 84 A3 11 18 11 10 19 14 21 12 14 83 A3 13 18 15 9 19 17 21 13 15 71 A3 9 18 8 10 20 11 16 9 16 90 A3 11 18 11 7 19 15 17 12 15 57 A4 11 18 13 9 19 14 20 12 14 57 A4 12 18 13 8 19 14 20 12 14 7 A8 13 13 8 12 13 17 21 13 13 40 A8 14 12 9 10 12 20 21 14 12 91 A8 14 12 13 11 13 15 14 11 6 A10 12 11 10 12 11 15 19 13 16 6 A10 12 11 11 12 11 15 19 13 17 6 A10 12 11 10 12 11 15 19 13 17 11 Al0 10 12 11 12 12 13 20 11 17 44 Al0 10 9 15 10 10 13 16 11 13 55 Al0 10 8 15 10 9 13 16 11 13 74 A10 12 8 11 10 9 15 16 12 14 13 A10 10 11 14 9 11 12 16 11 12 34 A11 13 11 10 14 18 12 10 73 A11 10 11 12 13 18 10 9

TABLE 37 A5 Systems D & E: sequence aligment mismach evaluation Reference of sequence: HPV 56->ref|NC_001594.1| System D System E forward reverse forward reverse primer primer probe primer primer probe SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 9 NO: 14 NO: 24 NO: 10 NO: 15 NO: 24 N^(o)HPV Group A5E6f4 A5E6r4 A5E6s4 A5E6f5 A5E6r5 A5E6s4 51 A5 0 0 0 0 0 0 26 A5 5 3 6 7 4 6 69 A5 6 3 7 7 5 7 82 A5 1 0 3 3 3 3 56 A6 6 5 13 7 6 13 30 A6 8 1 13 10 4 13 53 A6 8 3 12 8 6 12 66 A6 7 5 13 7 6 13 18 A7 15 3 11 13 8 11 39 A7 14 4 11 12 5 11 45 A7 15 4 12 13 6 12 59 A7 16 4 11 12 5 11 68 A7 15 4 11 13 8 11 85 A7 17 4 13 14 6 13 70 A7 14 4 13 12 7 13 16 A9 13 9 14 9 8 14 16 A9 13 9 14 9 8 14 31 A9 12 4 14 8 6 14 33 A9 13 6 15 9 7 15 35 A9 14 6 12 10 9 12 52 A9 12 4 13 7 6 13 58 A9 12 6 16 8 5 16 67 A9 13 6 17 9 7 17 54 A 18 2 11 14 11 42 A1 42 6 13 7 13 32 A1 12 6 13 8 13 61 A3 15 10 12 8 12 72 A3 16 12 10 9 10 89 A3 18 13 18 11 8 18 86 A3 17 10 14 7 14 87 A3 18 11 14 7 14 84 A3 17 13 13 8 13 83 A3 17 11 14 11 10 14 71 A3 17 15 11 6 11 90 A3 17 13 10 8 10 57 A4 17 14 11 10 11 57 A4 17 14 12 10 12 7 A8 24 3 11 7 11 40 A8 24 4 13 6 13 91 A8 18 1 14 10 14 6 A10 19 4 12 10 12 6 A10 20 4 12 10 12 6 A10 20 4 12 10 12 11 A10 19 4 10 9 10 44 A10 21 9 12 11 12 55 A10 21 9 12 11 12 74 A10 18 9 15 10 15 13 A10 32 6 12 10 12 34 A11 42 15 13 15 9 13 73 A11 42 15 10 14 9 10

TABLE 38 A6 Systems A to C: sequence aligment mismach evaluation Reference of sequence: HPV 56->ref|NC_001594.1| System A System B System C forward reverse forward reverse forward reverse primer primer probe primer primer probe primer primer probe SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 30 NO: 35 NO: 41 NO: 31 NO: 35 NO: 41 NO: 32 NO: 36 NO: 42 N^(o)HPV Group A6E6f1 A6E6r1 A6E6s1 A6E6f2 A6E6r1 A6E6s1 A6E6f3 A6E6r2 A6E6s2 51 A5 9 7 17 8 7 17 3 14 9 26 A5 9 10 19 10 10 19 4 13 11 69 A5 10 11 16 10 11 16 5 11 11 82 A5 10 8 18 9 8 18 4 14 9 56 A6 0 0 0 0 0 0 0 0 0 30 A6 4 8 16 7 8 16 2 10 8 53 A6 5 7 14 7 7 14 2 10 8 66 A6 2 2 6 6 2 6 2 6 6 18 A7 14 7 21 14 7 21 8 22 15 39 A7 11 9 23 10 9 23 8 22 10 45 A7 13 8 22 15 8 22 8 22 16 59 A7 10 9 20 13 9 20 7 22 14 68 A7 12 9 25 11 9 25 9 22 11 85 A7 12 8 22 12 8 22 6 22 13 70 A7 13 8 23 9 8 23 8 22 10 16 A9 6 9 17 10 9 17 8 13 11 16 A9 6 9 17 10 9 17 8 13 11 31 A9 9 6 21 10 6 21 7 16 12 33 A9 8 10 16 11 10 16 6 16 11 35 A9 8 7 18 12 7 18 7 14 13 52 A9 7 10 23 11 10 23 9 14 11 58 A9 8 9 18 10 9 18 8 14 10 67 A9 8 9 23 9 9 23 7 15 9 54 A 10 10 30 14 10 30 8 18 16 42 A1 9 9 11 9 9 20 12 32 A1 10 5 9 5 9 20 11 61 A3 9 8 11 8 10 21 13 72 A3 10 8 13 8 9 21 15 89 A3 9 10 10 10 9 18 10 86 A3 11 10 9 10 10 18 9 87 A3 11 10 10 10 9 17 12 84 A3 9 9 10 9 9 18 12 83 A3 10 10 10 10 10 18 10 71 A3 10 12 9 12 6 18 9 90 A3 10 8 11 8 8 18 12 57 A4 8 10 10 10 8 18 12 57 A4 8 9 9 9 8 18 11 7 A8 6 7 11 7 6 18 13 40 A8 7 7 10 7 8 18 13 91 A8 10 8 12 8 11 19 14 6 A10 11 12 14 12 7 16 18 6 A10 11 12 14 12 7 16 17 6 Al0 11 12 14 12 7 16 18 11 A10 10 11 13 11 9 16 17 44 A10 10 12 11 12 9 17 14 55 A10 10 10 12 10 10 17 14 74 A10 9 11 12 11 8 16 14 13 A10 9 9 12 9 9 18 14 34 A11 9 7 25 6 7 25 6 15 7 73 A11 8 7 24 6 7 24 6 15 6

TABLE 39 A6 Systems D & E: sequence aligment mismach evaluation Reference of sequence: HPV 56->ref|NC_001594.1| System D System E forward reverse forward reverse primer primer probe primer primer probe SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 33 NO: 35 NO: 41 NO: 34 NO: 37 NO: 44 N^(o)HPV Group A6E6f4 A6E6r1 A6E6s1 A6E6f5 A6E6r3 A6E6s3 51 A5 8 7 17 11 9 26 A5 10 10 19 8 9 69 A5 11 11 16 8 8 82 A5 10 8 18 9 9 56 A6 0 0 0 0 0 30 A6 5 8 16 6 1 53 A6 6 7 14 6 2 66 A6 3 2 6 3 0 18 A7 15 7 21 13 12 39 A7 12 9 23 10 13 45 A7 14 8 22 13 15 59 A7 12 9 20 10 15 68 A7 13 9 25 10 12 85 A7 14 8 22 10 12 70 A7 13 8 23 9 12 16 A9 6 9 17 9 16 A9 6 9 17 9 31 A9 9 6 21 9 33 A9 7 10 16 13 35 A9 8 7 18 14 52 A9 6 10 23 15 58 A9 7 9 18 14 67 A9 7 9 23 12 54 A 10 10 30 13 42 A1 10 9 13 32 A1 10 5 14 61 A3 10 8 11 13 72 A3 11 8 14 14 89 A3 10 10 11 12 86 A3 12 10 13 15 87 A3 12 10 14 13 84 A3 10 9 13 13 83 A3 11 10 16 14 71 A3 10 12 14 16 90 A3 10 8 13 13 57 A4 9 10 12 57 A4 9 9 12 7 A8 7 7 12 14 40 A8 8 7 8 14 91 A8 11 8 14 14 6 A10 12 12 14 6 A10 12 12 14 6 A10 12 12 14 11 A10 11 11 14 44 A10 11 12 13 55 A10 11 10 13 74 A10 10 11 12 13 A10 8 9 14 34 A11 10 7 25 13 73 A11 10 7 24 12

TABLE 40 A7 Systems A & B: sequence alignment mismach evaluation Reference of sequence: HPV 18->gi|9626069|ref|NC_001357.1| System A SEQ forward reverse ID primer primer probes N^(o) NO: 

68 69 70 79 80 81 102 103 104 105 106 HPV Group 

6f1a 6f2a 6f3a 6r1b 6r2b 6r3b A7E1ZAS61f A7E1ZAS63f A7E1ZAS64f A7E1ZCS40f A7E1ZBS74f 51 A5 4 5 4 7 5 5 5 5 4 4 9 26 A5 7 5 4 7 7 7 4 3 4 3 8 69 A5 5 6 6 7 7 6 4 3 4 3 8 82 A5 3 4 3 7 7 7 6 6 5 5 10 56 A6 5 5 3 5 8 9 5 6 7 6 9 30 A6 8 6 4 7 8 7 4 3 3 3 13 53 A6 8 4 6 6 7 8 6 6 4 5 10 66 A6 5 5 3 5 10 8 5 6 7 6 11 18 A7 0 2 2 1 5 6 0 3 4 1 4 39 A7 4 1 3 3 0 4 4 4 0 3 1 45 A7 2 0 2 1 3 6 1 2 3 0 6 59 A7 3 2 0 6 4 0 3 0 4 2 5 68 A7 1 2 2 4 1 3 2 2 2 1 0 85 A7 1 3 3 5 2 4 5 3 3 4 3 70 A7 3 5 3 5 2 2 6 4 4 5 2 16 A9 2 2 4 5 7 5 7 4 7 6 9 16 A9 3 3 3 5 7 5 7 4 7 6 9 31 A9 3 5 2 6 7 6 8 5 7 7 10 33 A9 4 5 3 5 3 5 7 4 5 6 7 35 A9 4 5 3 6 7 5 5 3 5 4 10 52 A9 4 3 3 5 5 6 5 3 3 4 9 58 A9 3 5 3 6 4 4 5 2 4 4 8 67 A9 2 4 2 5 4 5 5 3 4 4 6 54 A 7 9 8 10  9 9 9 9 9 9 10 42 A1 3 7 5 4 6 6 7 4 4 6 12 32 A1 4 6 6 7 7 7 7 4 5 6 12 61 A3 6 11  9 10  9 12  6 5 7 5 13 72 A3 4 10  7 11  9 13  5 5 6 6 13 89 A3 4 10  7 9 10 13  6 4 5 5 13 86 A3 9 9 9 10  9 12  6 6 7 7 12 87 A3 8 9 8 11  9 11  8 6 5 7 12 84 A3 5 9 7 12  12 14  5 4 6 4 12 83 A3 6 11  10  10  10 10  7 8 7 9 12 71 A3 10  13  12  8 6 7 6 5 7 5 13 90 A3 7 8 7 8 7 7 7 6 8 6 13 57 A4 10  12  11  7 9 12  6 9 8 7 14 57 A4 10  12  11  18  20 21  6 9 8 7 14  7 A8 6 9 7 9 9 8 5 3 4 4 14 40 A8 6 10 7 8 10 10  6 5 6 6 15 91 A8 7 8 8 9 10 9 7 5 5 6 15  6 A10 4 6 7 9 8 9 7 6 6 6 11  6 A10 4 6 7 9 8 9 7 6 6 6 11  6 A10 4 6 7 9 8 9 7 6 6 6 12 11 A10 4 8 7 6 9 12  6 6 3 5 10 44 A10 5 6 7 8 11 8 6 5 4 5 12 55 A10 6 7 8 9 11 9 6 5 4 5 12 74 A10 8 10  11  8 12 10  6 5 4 5 10 13 A10 4 5 5 9 9 9 4 6 3 5 9 34 A11 6 6 7 8 8 9 7 5 6 6 10 73 A11 4 4 6 9 6 10  7 5 6 6 6 System B SEQ forward reverse ID primer primer probes N^(o) NO: 

71 72 73 82 83 107 106 108 109 110 HPV Group 

15f1a 15f2a 15f3d 15r1a 15r2b A7E1ZBS26f A7E1ZBS74f A7E1ZBS79f A7E1ZBS80f A7E1ZBS27f 51 A5 4 5 6 5 3 6 9 8 8 6 26 A5 7 5 8 4 3 7 8 9 9 7 69 A5 5 6 8 4 3 6 8 8 8 7 82 A5 3 4 6 6 4 7 10 5 5 9 56 A6 5 5 9 5 6 7 9 10 10 7 30 A6 8 5 11 4 3 8 13 10 10 10 53 A6 8 7 7 6 4 10 10 10 10 10 66 A6 5 5 9 5 6 8 11 12 12 8 18 A7 0 3 4 0 2 0 4 6 6 2 39 A7 4 5 0 4 2 8 1 4 4 8 45 A7 2 3 2 1 1 1 6 8 8 0 59 A7 3 0 5 2 2 5 5 0 0 7 68 A7 1 3 4 2 0 6 0 5 5 6 85 A7 1 4 4 4 3 7 3 6 6 7 70 A7 3 3 6 5 4 8 2 5 5 8 16 A9 2 5 4 6 6 7 9 9 9 7 16 A9 3 4 5 6 6 7 9 9 9 7 31 A9 3 1 6 7 7 7 10 10 10 8 33 A9 4 4 7 6 6 8 7 8 8 8 35 A9 4 5 8 4 3 9 10 8 8 10 52 A9 4 4 5 4 3 7 9 8 8 8 58 A9 3 4 7 4 4 9 8 9 9 9 67 A9 2 3 6 4 3 7 6 7 7 7 54 A 9 6 8 8 9 6 10 9 9 8 42 A1 5 5 6 6 6 7 12 11 11 9 32 A1 6 6 5 6 6 7 12 10 10 8 61 A3 8 6 8 5 6 11 13 13 13 12 72 A3 6 5 8 4 5 13 13 11 11 14 89 A3 6 5 8 5 4 10 13 11 11 12 86 A3 11  6 8 5 6 12 12 12 12 13 87 A3 10  5 9 7 6 10 12 12 12 11 84 A3 7 4 7 4 5 9 12 12 12 10 83 A3 8 6 7 6 8 10 12 13 13 12 71 A3 12  10  11 5 6 8 13 10 10 10 90 A3 9 6 8 6 7 8 13 10 10 10 57 A4 12  8 11 6 8 11 14 12 12 12 57 A4 12  8 11 6 8 11 14 12 12 12  7 A8 8 6 9 4 3 12 14 12 12 13 40 A8 8 6 9 5 5 11 15 10 10 12 91 A8 9 8 9 6 5 10 15 12 12 11  6 A10 6 7 3 7 6 8 11 11 11 8  6 A10 6 7 3 7 6 8 11 11 11 8  6 A10 6 7 3 7 6 8 12 11 11 8 11 A10 6 6 6 6 4 9 10 11 11 9 44 A10 7 6 5 6 5 8 12 11 11 10 55 A10 8 7 6 6 5 9 12 11 11 11 74 A10 10  10  8 6 5 9 10 12 12 9 13 A10 6 5 5 4 4 9 9 10 10 9 34 A11 6 6 8 6 5 10 10 10 10 10 73 A11 4 7 6 6 5 8 6 7 7 8

TABLE 41 A7 Systems C & D: sequence aligment mismach evaluation Reference of sequence: HPV 18 ->gi|9626069|ref|NC_001357.1| System C System D SEQ ID forward primer reverse primer probes forward primer NO: 

74 75 76 84 85 111 105 112 113 114 77 78 N^(o)HPV Group 

A7E17f1 A7E17f2 A7E1f3 A7E17r1 A7E17r2 A7E1ZCS11f A7E1ZCS40f A7E1ZCS45f A7E1ZCS63f A7E1ZCS90f A7E12f1 A7E12f2 51 A5 7 7 10 5 5 4 4 4 5 6 8 7 26 A5 7 8 9 5 7 3 3 4 3 4 9 7 69 A5 7 6 9 5 8 3 3 4 3 4 8 6 82 A5 7 6 9 7 7 5 5 5 6 7 8 6 56 A6 8 7 9 6 9 6 6 7 6 5 6 5 30 A6 9 8 12 6 7 3 3 3 3 3 6 6 53 A6 11 8 10 5 8 5 5 4 6 5 6 6 66 A6 9 10 11 5 9 6 6 7 6 5 6 5 18 A7 0 6 5 1 6 1 1 4 3 3 1 5 39 A7 8 2 1 3 2 3 3 0 4 4 3 1 45 A7 2 7 7 1 4 0 0 3 2 3 2 6 59 A7 5 2 5 4 2 2 2 4 0 2 3 4 68 A7 6 2 0 4 1 1 1 2 2 0 5 1 85 A7 7 3 3 5 2 4 4 3 3 4 3 3 70 A7 8 4 2 3 2 5 5 4 4 4 5 1 16 A9 7 7 10 3 6 6 6 7 4 6 6 10 16 A9 7 7 10 3 6 6 6 7 4 6 6 10 31 A9 7 10 11 4 7 7 7 7 5 6 3 5 33 A9 8 8 8 5 3 6 6 5 4 4 3 3 35 A9 9 5 10 4 6 4 4 5 3 4 4 7 52 A9 8 8 10 6 5 4 4 3 3 4 5 5 58 A9 9 9 9 5 3 4 4 4 2 4 5 6 67 A9 7 7 7 4 4 4 4 4 3 3 4 6 54 A 7 8 11 9 9 9 9 9 9 10  6 8 42 A1 8 8 13 4 6 6 6 4 4 6 8 10 32 A1 8 9 13 5 7 6 6 5 4 4 8 10 61 A3 11 14 14 10 11 5 5 7 5 3 16  13 72 A3 13 11 13 11 12 6 6 6 5 4 16  13 89 A3 10 9 12 9 12 5 5 5 4 4 16  14 86 A3 12 8 12 10 11 7 7 7 6 4 17  18 87 A3 10 8 13 11 10 7 7 5 6 4 18  19 84 A3 10 11 13 12 13 4 4 6 4 3 15  17 83 A3 10 10 13 10 10 9 9 7 8 9 17  18 71 A3 8 8 13 7 6 5 5 7 5 5 16  16 90 A3 8 8 13 7 6 6 6 8 6 6 17  16 57 A4 11 11 14 8 11 7 7 8 9 8 15  16 57 A4 11 11 14 8 11 7 7 8 9 8 15  16 7 A8 12 14 15 8 8 4 4 4 3 5 8 9 40 A8 11 9 14 8 9 6 6 6 5 7 7 9 91 A8 11 12 15 8 9 6 6 5 5 6 5 8 6 A10 9 9 12 9 8 6 6 6 6 7 8 10 6 A10 9 9 12 9 8 6 6 6 6 7 8 10 6 A10 9 9 12 9 8 6 6 6 6 7 8 10 11 A10 9 9 11 8 11 5 5 3 6 7 8 10 44 A10 9 8 13 8 9 5 5 4 5 6 11  13 55 A10 9 9 13 8 10 5 5 4 5 6 11  13 74 A10 10 9 11 7 11 5 5 4 5 6 11  13 13 A10 10 9 10 10 8 5 5 3 6 6 10  11 34 A11 11 7 9 9 8 6 6 6 5 5 12  16 73 A11 8 5 6 8 9 6 6 6 5 5 12  16 System D SEQ ID reverse primer probes NO: 

86 87 115 116 117 118 119 120 121 N^(o)HPV Group 

A7E12r2 A7E12r3 A7E1ZDS36f A7E1ZDS37f A7E1ZDS38f A7E1ZDS2f A7E1ZDS3f A7E1ZDS4f A7E1ZDS11f 51 A5 2 4 4 6 4 4 3 3 3 26 A5 8 7 8 6 8 7 6 6 6 69 A5 9 8 7 7 7 6 6 6 6 82 A5 4 5 9 7 7 7 6 6 6 56 A6 8 11 9 9 6 8 8 8 8 30 A6 8 9 12 9 9 10 8 8 8 53 A6 11 12 12 11  9 10 11 11 11 66 A6 9 9 8 8 7 7 8 8 8 18 A7 3 0 6 0 5 3 5 5 5 39 A7 1 1 8 6 3 3 7 7 7 45 A7 2 2 0 6 5 5 0 0 0 59 A7 2 1 7 7 2 4 5 5 5 68 A7 1 3 5 3 2 0 4 4 4 85 A7 5 6 6 6 2 4 5 5 5 70 A7 2 1 7 7 4 4 6 6 6 16 A9 5 5 7 5 4 6 4 4 4 16 A9 5 5 6 6 5 7 3 3 3 31 A9 7 9 6 6 6 6 5 5 5 33 A9 3 7 8 8 8 8 6 6 6 35 A9 4 6 3 3 3 3 3 52 A9 1 6 8 7 7 8 7 7 7 58 A9 4 8 8 7 9 9 6 6 6 67 A9 2 5 7 7 6 5 6 6 6 54 A 6 9 4 6 3 3 3 3 3 42 A1 4 7 7 6 6 6 5 5 5 32 A1 2 6 6 7 6 6 5 5 5 61 A3 9 7 12 12  12  11 11 11 11 72 A3 9 10 12 11  9 9 11 11 11 89 A3 13 14 12 11  10  10 10 10 10 86 A3 9 7 11 11  11  10 10 10 10 87 A3 11 11 13 13  13  12 12 12 12 84 A3 10 8 11 11  10  9 10 10 10 83 A3 11 10 11 12  11  10 11 11 11 71 A3 9 10 9 8 9 8 9 9 9 90 A3 11 12 12 10  13  11 12 12 12 57 A4 10 7 11 11  13  12 10 10 10 57 A4 11 8 11 11  13  12 10 10 10 7 A8 8 11 11 10  8 9 7 7 7 40 A8 9 13 11 10  10  9 8 8 8 91 A8 10 12 9 9 9 10 7 7 7 6 A10 5 10 8 7 7 6 6 6 6 6 A10 5 10 8 7 7 6 6 6 6 6 A10 5 10 8 7 7 6 6 6 6 11 A10 6 10 8 8 7 6 6 6 6 44 A10 5 12 11 10  8 9 9 9 9 55 A10 6 12 9 10  8 9 6 6 6 74 A10 3 9 8 9 8 7 7 7 7 13 A10 4 9 11 10  8 9 8 8 8 34 A11 8 10 9 7 8 7 7 7 7 73 A11 6 9 8 6 7 6 6 6 6

TABLE 42 A9 System C: sequence aligment mismach evaluation Reference of sequence: HPV 16->gi|9627100|ref|NC_001526.1| forward reverse primer primer probes 211 212 213 214 215 216 217 240 241 283 284 285 N^(o)HPV Group A9E1f7 A9E1f8 A9E1f9 A9E1f10 A9E1f11 A9E1f12 A9E1f13 A9E1r5 A9E1r6 A9E1S1

A9E1S1

A9E1S1

51 A5 5 6 7 5 5 6 6 2 6 4 4 4 26 A5 5 6 7 5 5 6 6 3 5 6 6 6 69 A5 5 6 7 5 5 6 6 3 5 6 6 6 82 A5 5 6 7 5 5 6 6 2 6 4 4 4 56 A6 1 2 3 1 3 2 4 3 5 3 3 3 30 A6 3 4 5 3 3 4 4 4 6 3 3 5 53 A6 3 4 5 3 3 4 4 4 6 2 2 4 66 A6 2 3 4 2 4 3 5 4 6 3 3 3 18 A7 3 4 5 3 3 4 4 7 4 9 9 9 39 A7 6 5 6 5 4 5 5 2 4 9 9 9 45 A7 3 4 5 3 3 4 4 4 4 9 9 9 59 A7 3 2 3 1 1 2 2 5 7 9 9 9 68 A7 13 12 13 11 13 12 14 16 17 17 17 17 85 A7 2 3 4 2 2 3 3 3 5 5 5 5 70 A7 7 6 5 5 5 4 4 4 4 9 9 9 16 A9 0 1 2 2 2 3 3 0 5 1 1 3 16 A9 0 1 2 2 2 3 3 0 5 1 1 3 31 A9 2 1 2 0 1 1 3 0 5 1 1 1 33 A9 4 3 2 2 3 1 1 6 1 1 1 3 35 A9 2 1 2 0 2 1 3 1 6 3 3 1 52 A9 4 3 2 2 2 1 1 6 1 0 0 2 58 A9 4 3 2 4 2 3 1 6 1 0 0 2 67 A9 5 4 3 3 3 2 2 6 1 1 1 3 54 A 9 10 11 10 9 11 10 3 7 9 9 11 42 A1 6 7 8 6 6 7 7 5 7 3 3 5 32 A1 6 7 8 6 6 7 7 5 7 4 4 6 61 A3 12 13 14 12 12 13 13 4 6 9 9 11 72 A3 12 13 14 12 12 13 13 4 6 9 9 11 89 A3 9 10 11 9 9 10 10 4 6 8 8 10 86 A3 7 8 9 7 7 8 8 3 5 9 9 11 87 A3 7 8 9 7 7 8 8 3 5 11 11 13 84 A3 8 9 10 8 8 9 9 4 6 11 11 13 83 A3 9 10 11 9 9 10 10 4 6 9 9 11 71 A3 9 10 11 9 9 10 10 4 6 7 7 9 90 A3 9 10 11 9 9 10 10 4 6 6 6 8 57 A4 8 9 10 8 8 9 9 4 6 4 4 6 57 A4 8 9 10 8 8 9 9 4 6 4 4 6  7 A8 9 10 11 9 9 10 10 7 11 7 7 9 40 A8 10 11 12 10 10 11 11 7 11 9 9 11 91 A8 12 13 14 12 12 13 13 6 10 9 9 9  6 A10 11 12 13 11 11 12 12 5 7 5 5 7  6 A10 11 12 13 11 11 12 12 5 7 5 5 7  6 A10 11 12 13 11 11 12 12 5 7 6 6 8 11 A10 10 11 12 10 10 11 11 5 7 5 5 7 44 A10 12 13 14 12 12 13 13 5 9 6 6 8 55 A10 13 14 15 13 13 14 14 5 9 7 7 9 74 A10 13 14 15 13 13 14 14 5 9 6 6 8 13 A10 12 13 14 12 12 13 13 6 8 7 7 9 34 A11 6 7 6 6 6 7 5 3 6 3 3 5 73 A11 7 8 7 7 7 8 6 3 6 3 3 5 probes 286 287 288 289 290 291 292 293 294 295 N^(o)HPV Group A9E1S1

A9E1S12 A9E1S12a A9E1S12b A9E1S1

A9E1S1

A9E1S13c A9E1S1

A9E1S1

A9E1S1

51 A5 4 4 4 4 3 3 3 3 4 4 26 A5 6 6 6 6 5 5 5 4 6 6 69 A5 6 6 6 6 5 5 5 4 6 6 82 A5 4 4 4 4 3 3 3 3 4 4 56 A6 3 4 4 4 3 3 3 1 4 4 30 A6 5 6 6 6 5 5 5 3 6 6 53 A6 4 5 5 5 4 4 4 2 5 5 66 A6 3 4 4 4 3 3 3 1 4 4 18 A7 9 10 10 10 10 10 10 9 11 11 39 A7 9 10 10 10 9 9 9 9 10 10 45 A7 9 10 10 10 13 13 13 11 13 13 59 A7 9 8 8 8 8 8 8 9 9 9 68 A7 17 17 17 17 20 20 20 18 22 22 85 A7 5 4 4 4 7 7 7 8 7 7 70 A7 9 10 10 10 8 3 8 8 9 9 16 A9 3 4 4 4 3 3 3 1 4 4 16 A9 3 4 4 4 3 3 3 1 4 4 31 A9 1 2 2 2 1 1 1 0 2 2 33 A9 3 4 4 4 4 4 4 3 4 4 35 A9 1 0 0 0 1 1 1 2 0 0 52 A9 2 3 3 3 3 3 3 2 3 3 58 A9 2 3 3 3 3 3 3 2 3 3 67 A9 3 4 4 4 4 4 4 3 4 4 54 A 11 11 11 11 12 12 12 11 13 13 42 A1 5 6 6 6 5 5 5 4 7 7 32 A1 6 6 6 6 5 5 5 5 7 7 61 A3 11 11 11 11 20 20 20 20 20 20 72 A3 11 10 10 10 19 19 19 19 19 19 89 A3 10 10 10 10 20 20 20 19 20 20 86 A3 11 11 11 11 21 21 21 19 22 22 87 A3 13 13 13 13 18 18 18 16 18 18 84 A3 13 13 13 13 18 18 18 17 19 19 83 A3 11 11 11 11 19 19 19 18 19 19 71 A3 9 10 10 10 13 13 13 11 14 14 90 A3 8 9 9 9 12 12 12 10 13 13 57 A4 6 7 7 7 11 11 11 10 13 13 57 A4 6 7 7 7 11 11 11 10 13 13  7 A8 9 9 9 9 8 8 8 8 10 10 40 A8 11 11 11 11 10 10 10 9 12 12 91 A8 9 9 9 9 8 8 8 8 10 10  6 A10 7 7 7 7 8 8 8 8 9 9  6 A10 7 7 7 7 8 8 8 8 9 9  6 A10 8 8 8 8 9 9 9 8 10 10 11 A10 7 7 7 7 8 8 8 8 9 9 44 A10 8 8 8 8 7 7 7 7 9 9 55 A10 9 9 9 9 8 8 8 7 10 10 74 A10 8 8 8 8 7 7 7 7 9 9 13 A10 9 9 9 9 8 8 8 7 10 10 34 A11 5 4 4 4 3 3 3 3 4 4 73 A11 5 4 4 4 3 3 3 3 4 4

indicates data missing or illegible when filed

TABLE 43 A9 System E1: sequence aligment mismach evaluation Reference of sequence: HPV 16->gi||ref|NC_001526.1| forward primer reverse primer probes SEQ ID NO: 218 219 220 242 243 244 245 246 247 296 N^(o)HPV Group A9E2f1 A9E2f2 A9E2f4 A9E2r1 A9E2r2 A9E2r3 A9E2r4 A9E2r13 A9E2r14 A9E2Z7S1 51 A5 10 9 10 8 9 9 7 13 12 6 26 A5 11 13 11 9 6 6 9 10 15 5 69 A5 11 13 11 8 7 6 8 11 13 3 82 A5 9 9 10 8 7 5 5 12 14 3 56 A6 6 10 9 8 6 6 6 10 14 8 30 A6 6 7 9 8 8 8 10 13 14 6 53 A6 6 7 7 7 3 4 5 12 13 7 66 A6 8 11 9 7 6 6 7 9 11 9 18 A7 4 9 7 9 5 6 7 10 11 7 39 A7 4 9 7 7 4 5 6 12 10 8 45 A7 4 9 7 11 10 10 9 9 12 6 59 A7 4 9 8 7 4 5 8 9 10 6 68 A7 4 9 7 7 4 5 6 12 10 8 85 A7 5 8 9 8 4 5 5 9 10 7 70 A7 4 7 8 7 3 4 5 10 10 8 16 A9 0 8 8 0 5 6 8 9 11 0 16 A9 0 8 8 2 4 5 8 10 10 1 31 A9 7 10 3 8 9 9 10 0 10 2 33 A9 7 1 8 9 8 7 2 12 12 5 35 A9 3 9 6 6 8 9 9 11 0 8 52 A9 8 9 3 5 0 1 6 13 12 5 58 A9 9 2 10 8 3 2 3 10 8 5 67 A9 6 4 6 7 2 1 4 9 12 5 54 A 4 7 8 8 5 6 9 10 10 6 42 A1 9 11 11 9 7 8 7 12 13 5 32 A1 8 13 10 8 8 7 7 13 12 6 61 A3 7 10 8 8 6 7 9 13 15 6 72 A3 7 7 8 10 9 10 12 15 16 5 89 A3 5 7 6 8 8 8 11 13 12 6 86 A3 10 7 11 10 8 6 9 13 16 7 87 A3 9 5 12 10 8 7 10 15 15 7 84 A3 9 7 10 11 11 9 11 11 14 8 83 A3 9 10 9 7 10 10 9 11 11 7 71 A3 7 7 8 9 9 9 12 16 15 7 90 A3 9 10 9 12 13 11 11 13 13 9 57 A4 13 10 11 9 10 9 12 14 12 8 57 A4 13 8 11 9 10 9 12 15 13 8  7 A8 7 10 7 8 8 8 9 12 11 10 40 A8 8 11 5 9 11 10 9 12 11 10 91 A8 5 7 11 10 10 9 9 9 9 5  6 A10 8 9 9 9 6 5 8 11 11 8  6 A10 8 9 9 9 6 5 8 11 11 8  6 A10 8 9 9 9 6 5 8 11 11 8 11 A10 8 9 10 6 4 5 9 11 12 7 44 A10 8 9 10 6 6 5 5 13 13 5 55 A10 8 9 10 4 6 5 7 11 11 5 74 A10 9 9 11 8 5 4 5 12 12 4 13 A10 8 8 9 9 6 6 6 9 10 4 34 A11 9 7 9 8 7 8 9 11 16 6 73 A11 10 6 10 7 7 7 7 13 12 7 probes SEQ ID NO: 297 298 299 300 301 302 303 N^(o)HPV Group A9E2Z7S2 A9E2Z7S2a A9E2Z7S2b A9E2Z7S3 A9E2Z7S3a A9E2Z7S4 A9E2Z7S4a 51 A5 5 5 5 9 9 6 6 26 A5 3 3 3 6 6 4 4 69 A5 3 3 3 7 7 3 3 82 A5 3 3 3 7 7 3 3 56 A6 7 7 7 9 9 7 7 30 A6 6 6 6 9 9 7 7 53 A6 5 5 5 10 10 8 8 66 A6 8 8 8 10 10 8 8 18 A7 1 1 1 8 8 6 6 39 A7 4 4 4 8 8 6 6 45 A7 3 3 3 10 10 6 6 59 A7 3 3 3 7 7 5 5 68 A7 4 4 4 8 8 6 6 85 A7 6 6 6 10 10 5 5 70 A7 5 5 5 8 8 6 6 16 A9 6 6 6 8 8 4 4 16 A9 5 5 5 9 9 5 5 31 A9 4 4 4 6 6 1 1 33 A9 1 1 1 9 9 7 7 35 A9 8 8 8 0 0 6 6 52 A9 3 3 3 7 7 2 2 58 A9 1 1 1 7 7 5 5 67 A9 1 1 1 7 7 4 4 54 A 8 8 8 8 8 5 5 42 A1 6 6 6 8 8 4 4 32 A1 6 6 6 9 9 5 5 61 A3 6 6 6 7 7 5 5 72 A3 8 8 8 7 7 5 5 89 A3 6 6 6 8 8 7 7 86 A3 9 9 9 8 8 9 9 87 A3 8 8 8 7 7 8 8 84 A3 9 9 9 8 8 10 10 83 A3 8 8 8 9 9 8 8 71 A3 7 7 7 9 9 7 7 90 A3 8 8 8 9 9 9 9 57 A4 6 6 6 9 9 8 8 57 A4 6 6 6 9 9 8 8  7 A8 9 9 9 3 3 8 8 40 A8 9 9 9 4 4 9 9 91 A8 5 5 5 3 3 5 5  6 A10 7 7 7 11 11 8 8  6 A10 7 7 7 11 11 8 8  6 A10 7 7 7 11 11 8 8 11 A10 9 9 9 10 10 8 8 44 A10 9 9 9 7 7 8 8 55 A10 9 9 9 7 7 8 8 74 A10 7 7 7 8 8 6 6 13 A10 7 7 7 6 6 4 4 34 A11 6 6 6 7 7 5 5 73 A11 6 6 6 8 8 6 6

TABLE 44 A9 System E2: sequence aligment mismach evaluation Reference of sequence: HPV 16->gi||ref|NC_001526.1| forward primer reverse primer probes SEQ ID NO: 221 222 223 242 243 244 245 246 247 296 N^(o)HPV Group A9E2f1a A9E2f2a A9E2f4a A9E2r1 A9E2r2 A9E2r3 A9E2r4 A9E2r13 A9E2r14 A9E2Z7S1 51 A5 11 9 11 8 9 9 7 13 12 6 26 A5 13 14 11 9 6 6 9 10 15 5 69 A5 12 13 12 8 7 6 8 11 13 3 82 A5 10 9 11 8 7 5 5 12 14 3 56 A6 7 10 10 8 6 6 6 10 14 8 30 A6 7 7 10 8 8 8 10 13 14 6 53 A6 7 7 8 7 3 4 5 12 13 7 66 A6 9 11 10 7 6 6 7 9 11 9 18 A7 5 9 8 9 5 6 7 10 11 7 39 A7 5 9 8 7 4 5 6 12 10 8 45 A7 6 10 7 11 10 10 9 9 12 6 59 A7 6 10 8 7 4 5 8 9 10 6 68 A7 7 4 5 6 12 10 8 85 A7 7 9 9 8 4 5 5 9 10 7 70 A7 5 7 9 7 3 4 5 10 10 8 16 A9 1 8 9 0 5 6 8 9 11 0 16 A9 1 8 9 2 4 5 8 10 10 1 31 A9 7 11 3 8 9 9 10 0 10 2 33 A9 8 1 9 9 8 7 2 12 12 5 35 A9 2 9 7 6 8 9 9 11 0 8 52 A9 9 10 3 5 0 1 6 13 12 5 58 A9 10 2 11 8 3 2 3 10 8 5 67 A9 7 4 7 7 2 1 4 9 12 5 54 A 6 8 8 8 5 6 9 10 10 6 42 A1 10 11 12 9 7 8 7 12 13 5 32 A1 10 14 10 8 8 7 7 13 12 6 61 A3 9 11 8 8 6 7 9 13 15 6 72 A3 8 7 9 10 9 10 12 15 16 5 89 A3 7 8 6 8 8 8 11 13 12 6 86 A3 12 8 11 10 8 8 9 13 16 7 87 A3 11 6 12 10 8 7 10 15 15 7 84 A3 11 8 10 11 11 9 11 11 14 8 83 A3 11 11 9 7 10 10 9 11 11 7 71 A3 9 8 8 9 9 9 12 16 15 7 90 A3 11 11 9 12 13 11 11 13 13 9 57 A4 15 11 11 9 10 9 12 14 12 8 57 A4 15 9 11 9 10 9 12 15 13 8  7 A8 9 11 8 8 8 8 9 12 11 10 40 A8 8 12 6 9 11 10 9 12 11 10 91 A8 7 8 12 10 10 9 9 9 9 5  6 A10 8 10 10 9 6 5 8 11 11 8  6 A10 8 10 10 9 6 5 8 11 11 8  6 A10 3 10 10 9 6 5 8 11 11 8 11 A10 8 10 11 6 4 5 9 11 12 7 44 A10 8 10 11 6 6 5 5 13 13 5 55 A10 8 10 11 4 6 5 7 11 11 5 74 A10 10 10 12 8 5 4 5 12 12 4 13 A10 8 9 10 9 6 6 6 9 10 4 34 A11 10 7 10 8 7 8 9 11 16 6 73 A11 11 6 11 7 7 7 7 13 12 7 probes SEQ ID NO: 297 298 299 300 301 302 303 N^(o)HPV Group A9E2Z7S2 A9E2Z7S2a A9E2Z7S2b A9E2Z7S3 A9E2Z7S3a A9E2Z7S4 A9E2Z7S4a 51 A5 5 5 5 9 9 6 6 26 A5 3 3 3 6 6 4 4 69 A5 3 3 3 7 7 3 3 82 A5 3 3 3 7 7 3 3 56 A6 7 7 7 9 9 7 7 30 A6 6 6 6 9 9 7 7 53 A6 5 5 5 10 10 8 8 66 A6 8 8 8 10 10 8 8 18 A7 1 1 1 8 8 6 6 39 A7 4 4 4 8 8 6 6 45 A7 3 3 3 10 10 6 6 59 A7 3 3 3 7 7 5 5 68 A7 4 4 4 8 8 6 6 85 A7 6 6 6 10 10 5 5 70 A7 5 5 5 8 8 6 6 16 A9 6 6 6 8 8 4 4 16 A9 5 5 5 9 9 5 5 31 A9 4 4 4 6 6 1 1 33 A9 1 1 1 9 9 7 7 35 A9 8 8 8 0 0 6 6 52 A9 3 3 3 7 7 2 2 58 A9 1 1 1 7 7 5 5 67 A9 1 1 1 7 7 4 4 54 A 8 8 8 8 8 5 5 42 A1 6 6 6 8 8 4 4 32 A1 6 6 6 9 9 5 5 61 A3 6 6 6 7 7 5 5 72 A3 8 8 8 7 7 5 5 89 A3 6 6 6 8 8 7 7 86 A3 9 9 9 8 8 9 9 87 A3 8 8 8 7 7 8 8 84 A3 9 9 9 8 8 10 10 83 A3 8 8 8 9 9 8 8 71 A3 7 7 7 9 9 7 7 90 A3 8 8 8 9 9 9 9 57 A4 6 6 6 9 9 8 8 57 A4 6 6 6 9 9 8 8  7 A8 9 9 9 3 3 8 8 40 A8 9 9 9 4 4 9 9 91 A8 5 5 5 3 3 5 5  6 A10 7 7 7 11 11 8 8  6 A10 7 7 7 11 11 8 8  6 A10 7 7 7 11 11 8 8 11 A10 9 9 9 10 10 8 8 44 A10 9 9 9 7 7 8 8 55 A10 9 9 9 7 7 8 8 74 A10 7 7 7 8 8 6 6 13 A10 7 7 7 6 6 4 4 34 A11 6 6 6 7 7 5 5 73 A11 6 6 6 8 8 6 6

TABLE 45 A9 System E3: sequence aligment mismach evaluation Reference of sequence: HPV 16->gi||ref|NC_001526.1| forward primer reverse primer SEQ ID NO: 254 221 222 223 248 249 250 251 252 253 A9E- N^(o)HPV Group A9E2f1a A9E2f2a A9E2f4a A9E21r1cz A9E21r2az A9E21r3az A9E21r4fz A9E21r5az A9E21r6az 21r7az 51 A5 11 9 11 8 10 7 9 9 9 8 26 A5 13 14 11 9 7 11 13 7 6 6 69 A5 12 13 12 8 9 10 12 6 6 6 82 A5 10 9 11 8 10 5 12 6 5 6 56 A6 7 10 10 8 8 8 14 6 6 6 30 A6 7 7 10 8 11 12 14 9 8 8 53 A6 7 7 8 7 10 7 11 5 4 3 66 A6 9 11 10 7 8 9 11 6 6 6 18 A7 5 9 8 9 8 9 11 7 6 5 39 A7 5 9 8 7 9 8 8 6 5 4 45 A7 6 10 7 11 10 10 12 10 10 10 59 A7 6 10 8 7 8 10 9 6 5 4 68 A7 85 A7 7 9 9 8 8 7 8 6 5 4 70 A7 5 7 9 7 9 7 9 5 4 3 16 A9 1 8 9 0 8 9 10 7 6 5 16 A9 1 8 9 2 9 9 9 6 5 4 31 A9 7 11 3 8 0 12 11 10 9 9 33 A9 8 1 9 9 12 0 11 6 7 8 35 A9 2 9 7 6 8 9 0 10 9 8 52 A9 9 10 3 5 9 8 13 2 1 0 58 A9 10 2 11 8 9 5 11 1 2 3 67 A9 7 4 7 7 8 6 12 2 1 2 54 A 6 8 8 8 9 9 10 7 6 5 42 A1 10 11 12 9 8 9 12 7 8 7 32 A1 10 14 10 8 9 7 10 8 7 8 61 A3 9 11 8 8 10 9 13 8 7 6 72 A3 8 7 9 10 11 12 15 11 10 9 89 A3 7 8 6 8 10 11 11 9 8 7 86 A3 12 8 11 10 9 9 16 7 6 7 87 A3 11 6 12 10 9 10 16 8 7 8 84 A3 11 8 10 10 12 12 15 11 10 11 83 A3 11 11 9 7 10 9 10 9 10 9 71 A3 9 8 8 9 12 12 13 10 9 8 90 A3 11 11 9 12 11 12 12 12 12 12 57 A4 15 11 11 9 12 13 13 11 10 9 57 A4 15 9 11 9 12 13 14 11 10 9  7 A8 9 11 8 8 12 9 12 9 8 7 40 A8 8 12 6 9 12 10 12 12 11 11 91 A8 7 8 12 10 8 9 10 9 9 10  6 A10 8 10 10 9 10 8 11 6 5 6  6 A10 8 10 10 9 10 8 11 6 5 6  6 A10 8 10 10 9 10 8 11 6 5 6 11 A10 8 10 11 6 11 9 12 6 5 4 44 A10 8 10 11 6 11 5 13 6 5 6 55 A10 8 10 11 4 10 7 11 6 5 6 74 A10 10 10 12 8 10 5 12 5 4 5 13 A10 8 9 10 9 7 6 10 7 6 6 34 A11 10 7 10 8 7 9 13 9 8 7 73 A11 11 6 11 7 9 6 11 8 7 7 reverse primer probes SEQ ID NO: 255 296 297 298 299 300 301 302 303 N^(o)HPV Group A9E21r8az A9E2Z7S1 A9E2Z7S2 A9E2Z7S2a A9E2Z7S2b A9E2Z7S3 A9E2Z7S3a A9E2Z7S4 A9E2Z7S4a 51 A5 9 6 5 5 5 9 9 6 6 26 A5 8 5 3 3 3 6 6 4 4 69 A5 7 3 3 3 3 7 7 3 3 82 A5 7 3 3 3 3 7 7 3 3 56 A6 5 8 7 7 7 9 9 7 7 30 A6 10 6 6 6 6 9 9 7 7 53 A6 5 7 5 5 5 10 10 8 8 66 A6 6 9 8 8 8 10 10 8 8 18 A7 6 7 1 1 1 8 8 6 6 39 A7 6 8 4 4 4 8 8 6 6 45 A7 9 6 3 3 3 10 10 6 6 59 A7 6 6 3 3 3 7 7 5 5 68 A7 8 4 4 4 8 8 6 6 85 A7 5 7 6 6 6 10 10 5 5 70 A7 5 8 5 5 5 8 8 6 6 16 A9 8 0 6 6 6 8 8 4 4 16 A9 7 1 5 5 5 9 9 5 5 31 A9 9 2 4 4 4 6 6 1 1 33 A9 5 5 1 1 1 9 9 7 7 35 A9 10 8 8 8 8 0 0 6 6 52 A9 3 5 3 3 3 7 7 2 2 58 A9 0 5 1 1 1 7 7 5 5 67 A9 1 5 1 1 1 7 7 4 4 54 A 7 6 8 8 8 8 8 5 5 42 A1 6 5 6 6 6 8 8 4 4 32 A1 7 6 6 6 6 9 9 5 5 61 A3 7 6 6 6 6 7 7 5 5 72 A3 11 5 8 8 8 7 7 5 5 89 A3 9 6 6 6 6 8 8 7 7 86 A3 7 7 9 9 9 8 8 9 9 87 A3 8 7 8 8 8 7 7 8 8 84 A3 10 8 9 9 9 8 8 10 10 83 A3 9 7 8 8 8 9 9 8 8 71 A3 10 7 7 7 7 9 9 7 7 90 A3 11 9 8 8 8 9 9 9 9 57 A4 11 8 6 6 6 9 9 8 8 57 A4 11 8 6 6 6 9 9 8 8  7 A8 9 10 9 9 9 3 3 8 8 40 A8 11 10 9 9 9 4 4 9 9 91 A8 9 5 5 5 5 3 3 5 5  6 A10 6 8 7 7 7 11 11 8 8  6 A10 6 8 7 7 7 11 11 8 8  6 A10 6 8 7 7 7 11 11 8 8 11 A10 7 7 9 9 9 10 10 8 8 44 A10 6 5 9 9 9 7 7 8 8 55 A10 7 5 9 9 9 7 7 8 8 74 A10 4 4 7 7 7 8 8 6 6 13 A10 6 4 7 7 7 6 6 4 4 34 A11 8 6 6 6 6 7 7 5 5 73 A11 7 7 6 6 6 8 8 6 6

TABLE 46 A9 System E4: sequence aligment mismach evaluation forward primer reverse primer SEQ ID NO: 224 225 226 248 A9E- A9E- A9E- A9E- 249 250 251 252 253 254 N°HPV Group 2Z5Z6f1c 2Z5Z6f2c 2Z5Z6f3b 21r1cz A9E21r2az A9E21r3az A9E21r4fz A9E21r5az A9E21r6az A9E21r7az 51 A5 5 3 7 8 10 7 9 9 9 8 26 A5 7 7 5 9 7 11 13 7 6 6 69 A5 5 5 7 8 9 10 12 6 6 6 82 A5 5 4 7 8 10 5 12 6 5 6 58 A6 2 4 6 8 8 8 14 6 6 6 30 A6 2 2 6 8 11 12 14 9 8 8 53 A6 3 3 4 7 10 7 11 5 4 3 66 A6 4 5 6 7 8 9 11 6 6 6 18 A7 2 4 4 9 8 9 11 7 6 5 39 A7 2 4 4 7 9 8 8 6 5 4 45 A7 3 5 3 11 10 10 12 10 10 10 59 A7 3 5 3 7 8 10 9 6 5 4 68 A7 85 A7 4 4 4 8 8 7 8 6 5 4 70 A7 1 1 5 7 9 7 9 5 4 3 16 A9 1 3 5 0 8 9 10 7 6 5 16 A9 1 3 5 2 9 9 9 6 5 4 31 A9 2 4 2 8 0 12 11 10 9 9 33 A9 4 0 4 9 12 0 11 6 7 8 35 A9 0 2 4 6 8 9 0 10 9 8 52 A9 4 4 0 5 9 8 13 2 1 0 58 A9 5 2 6 8 9 5 11 1 2 3 67 A9 2 0 4 7 8 6 12 2 1 2 54 A 3 3 5 8 9 9 10 7 6 5 42 A1 6 6 7 9 8 9 12 7 8 7 32 A1 6 8 6 8 9 7 10 8 7 8 61 A3 6 6 2 8 10 9 13 8 7 6 72 A3 4 2 2 10 11 12 15 11 10 9 89 A3 6 6 2 8 10 11 11 9 8 7 86 A3 8 5 4 10 9 9 16 7 6 7 87 A3 9 5 4 10 9 10 16 8 7 8 84 A3 7 6 3 10 12 12 15 11 10 11 83 A3 8 7 4 7 10 9 10 9 10 9 71 A3 8 7 3 9 12 12 13 10 9 8 90 A3 10 9 5 12 11 12 12 12 12 12 57 A4 12 10 7 9 12 13 13 11 10 9 57 A4 12 10 7 9 12 13 14 11 10 9  7 A8 6 7 4 8 12 9 12 9 8 7 40 A8 4 5 4 9 12 10 12 12 11 11 91 A8 5 5 7 10 8 9 10 9 9 10  6 A10 6 5 8 9 10 8 11 6 5 6  6 A10 6 5 8 9 10 8 11 6 5 6  6 A10 6 5 8 9 10 8 11 6 5 6 11 A10 7 6 7 6 11 9 12 6 5 4 44 A10 6 6 8 6 11 5 13 6 5 6 55 A10 6 6 8 4 10 7 11 6 5 6 74 A10 5 5 7 8 10 5 12 5 4 5 13 A10 4 4 6 9 7 6 10 7 6 6 34 A11 5 3 5 8 7 9 13 9 8 7 73 A11 6 2 6 7 9 6 11 8 7 7 reverse primer probes SEQ ID NO: 255 296 297 298 299 300 301 302 303 N^(o)HPV Group A9E21r8az A9E2Z7S1 A9E2Z7S2 A9E2Z7S2a A9E2Z7S2b A9E2Z7S3 A9E2Z7S3a A9E2Z7S4 A9E2Z7S4a 51 A5 9 6 5 5 5 9 9 6 6 26 A5 8 5 3 3 3 6 6 4 4 69 A5 7 3 3 3 3 7 7 3 3 82 A5 7 3 3 3 3 7 7 3 3 56 A6 5 8 7 7 7 9 9 7 7 30 A6 10 6 6 6 6 9 9 7 7 53 A6 5 7 5 5 5 10 10 8 8 66 A6 6 9 8 8 8 10 10 8 8 18 A7 6 7 1 1 1 8 8 6 6 39 A7 6 8 4 4 4 8 8 6 6 45 A7 9 6 3 3 3 10 10 6 6 59 A7 6 6 3 3 3 7 7 5 5 68 A7 8 4 4 4 8 8 6 6 85 A7 5 7 6 6 6 10 10 5 5 70 A7 5 8 5 5 5 8 8 6 6 16 A9 8 0 6 6 6 8 8 4 4 16 A9 7 1 5 5 5 9 9 5 5 31 A9 9 2 4 4 4 6 6 1 1 33 A9 5 5 1 1 1 9 9 7 7 35 A9 10 8 8 8 8 0 0 6 6 52 A9 3 5 3 3 3 7 7 2 2 58 A9 0 5 1 1 1 7 7 5 5 67 A9 1 5 1 1 1 7 7 4 4 54 A 7 6 6 8 8 8 8 5 5 42 A1 6 5 6 6 6 8 8 4 4 32 A1 7 6 6 6 6 9 9 5 5 61 A3 7 6 6 6 6 7 7 5 5 72 A3 11 5 8 8 8 7 7 5 5 89 A3 9 6 6 6 6 8 8 7 7 86 A3 7 7 9 9 9 8 8 9 9 87 A3 8 7 8 8 8 7 7 8 8 84 A3 10 8 9 9 9 8 8 10 10 83 A3 9 7 8 8 8 9 9 8 8 71 A3 10 7 7 7 7 9 9 7 7 90 A3 11 9 8 8 8 9 9 9 9 57 A4 11 8 6 6 6 9 9 8 8 57 A4 11 8 6 6 6 9 9 8 8  7 A8 9 10 9 9 9 3 3 8 8 40 A8 11 10 9 9 9 4 4 9 9 91 A8 9 5 5 5 5 3 3 5 5  6 A10 6 8 7 7 7 11 11 8 8  6 A10 6 8 7 7 7 11 11 8 8  6 A10 6 8 7 7 7 11 11 8 8 11 A10 7 7 9 9 9 10 10 8 8 44 A10 6 5 9 9 9 7 7 8 8 55 A10 7 5 9 9 9 7 7 8 8 74 A10 4 4 7 7 7 8 8 6 6 13 A10 6 4 7 7 7 6 6 4 4 34 A11 8 6 6 6 6 7 7 5 5 73 A11 7 7 6 6 6 8 8 6 6

TABLE 47 A9 System F: sequence aligment mismach evaluation forward primer reverse primer SEQ ID 227 228 229 230 248 249 250 251 252 253 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

21f1az 21f2bz 21f3dz 21f4cz 21r1cz 21r2az 21r3az 21r4fz 21r5az 21r6az 51 A5  4  4  3 4  8 10  7  9  9  9 26 A5  3  3  5 2  9  7 11 13  7  6 69 A5  4  4  4 4  8  9 10 12  6  6 82 A5  6  6  4 6  8 10  5 12  6  5 56 A6  5  5  4 4  8  8  8 14  6  6 30 A6  6  4  2 5  8 11 12 14  9  8 53 A6  6  4  4 7  7 10  7 11  5  4 66 A6  3  3  3 4  7  8  9 11  6  6 18 A7  6  6  5 6  9  8  9 11  7  6 39 A7  6  6  5 6  7  9  8  8  6  5 45 A7  7  7  6 7 11 10 10 12 10 10 59 A7  9  8  6 9  7  8 10  9  6  5 68 A7 85 A7  5  3  5 4  8  8  7  8  6  5 70 A7  6  6  4 6  7  9  7  9  5  4 16 A9  0  2  5 3  0  8  9 10  7  6 16 A9  0  2  5 3  2  9  9  9  6  5 31 A9  3  1  5 5  8  0 12 11 10  9 33 A9  4  4  0 4  9 12  0 11  6  7 35 A9  2  0  4 5  6  8  9  0 10  9 52 A9  2  4  6 0  5  9  8 13  2  1 58 A9  4  4  2 3  8  9  5 11  1  2 67 A9  3  5  3 2  7  8  6 12  2  1 54 A  4  4  5 5  8  9  9 10  7  6 42 A1  7  8  6 6  9  8  9 12  7  8 32 A1  6  7  7 5  8  9  7 10  8  7 61 A3  4  2  6 3  8 10  9 13  8  7 72 A3  5  4  3 5 10 11 12 15 11 10 89 A3  7  6  8 8  8 10 11 11  9  8 86 A3  8  9  7 7 10  9  9 16  7  6 87 A3  8  8  6 6 10  9 10 16  8  7 84 A3  8  8  5 7 10 12 12 15 11 10 83 A3  7  5  6 6  7 10  9 10  9 10 71 A3  7  6  8 8  9 12 12 13 10  9 90 A3  8  6 10 7 12 11 12 12 12 12 57 A4  7  7  8 7  9 12 13 13 11 10 57 A4  6  6  9 6  9 12 13 14 11 10  7 A8  5  6  9 5  8 12  9 12  9  8 40 A8  6  6  6 7  9 12 10 12 12 11 91 A8  5  5  9 8 10  8  9 10  9  9  6 A10  6  8  5 6  9 10  8 11  6  5  6 A10  6  8  5 6  9 10  8 11  6  5  6 A10  7  8  5 7  9 10  8 11  6  5 11 A10  6  7  7 5  6 11  9 12  6  5 44 A10  3  5  7 4  6 11  5 13  6  5 55 A10  4  6  7 3  4 10  7 11  6  5 74 A10  6  6  6 5  8  0  5 12  5  4 13 A10  6  8  6 6  9  7  6 10  7  6 34 A11  6  6  5 6  8  7  9 13  9  8 73 A11  7  6  4 7  7  9  6 11  8  7 reverse primer probes SEQ ID 254 255 296 297 298 299 300 301 302 303 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

21r7az 21r8az 2Z7S1 2Z7S2 2Z7S2a 2Z7S2b 2Z7S3 2Z7S3a 2Z7S4 2Z7S4a 51 A5  8  9  5 5  5  5  9  9  6  6 26 A5  6  8  4 3  3  3  6  6  4  4 69 A5  6  7  2 3  3  3  7  7  3  3 82 A5  6  7  2 3  3  3  7  7  3  3 56 A6  6  5  7 7  7  7  9  9  7  7 30 A6  8 10  5 6  6  6  9  9  7  7 53 A6  3  5  7 5  5  5 10 10  8  8 66 A6  6  6  8 8  8  8 10 10  8  8 18 A7  5  6  6 1  1  1  8  8  6  6 39 A7  4  6  7 4  4  4  8  8  6  6 45 A7 10  9  5 3  3  3 10 10  6  6 59 A7  4  6  5 3  3  3  7  7  5  5 68 A7 4  4  4  8  8  6  6 85 A7  4  5  6 6  6  6 10 10  5  5 70 A7  3  5  7 5  5  5  8  8  6  6 16 A9  5  8  0 6  6  6  8  8  4  4 16 A9  4  7  1 5  5  5  9  9  5  5 31 A9  9  9  1 4  4  4  6  6  1  1 33 A9  8  5  5 1  1  1  9  9  7  7 35 A9  8 10  7 8  8  8  0  0  6  6 52 A9  0  3  4 3  3  3  7  7  2  2 58 A9  3  0  4 1  1  1  7  7  5  5 67 A9  2  1  4 1  1  1  7  7  4  4 54 A  5  7  5 8  8  8  8  8  5  5 42 A1  7  6  4 6  6  6  8  8  4  4 32 A1  8  7  5 6  6  6  9  9  5  5 61 A3  6  7  5 6  6  6  7  7  5  5 72 A3  9 11  4 8  8  8  7  7  5  5 89 A3  7  9  5 6  6  6  8  8  7  7 86 A3  7  7  6 9  9  9  8  8  9  9 87 A3  8  8  6 8  8  8  7  7  8  8 84 A3 11 10  7 9  9  9  8  8 10 10 83 A3  9  9  6 8  8  8  9  9  8  8 71 A3  8 10  6 7  7  7  9  9  7  7 90 A3 12 11  8 8  8  8  9  9  9  9 57 A4  9 11  7 6  6  6  9  9  8  8 57 A4  9 11  7 6  6  6  9  9  8  8  7 A8  7  9  9 9  9  9  3  3  8  8 40 A8 11 11  9 9  9  9  4  4  9  9 91 A8 10  9  4 5  5  5  3  3  5  5  6 A10  6  6  7 7  7  7 11 11  8  8  6 A10  6  6  7 7  7  7 11 11  8  8  6 A10  6  6  7 7  7  7 11 11  8  8 11 A10  4  7  6 9  9  9 10 10  8  8 44 A10  6  6  5 9  9  9  7  7  8  8 55 A10  6  7  5 9  9  9  7  7  8  8 74 A10  5  4  4 7  7  7  8  8  6  6 13 A10  6  6  3 7  7  7  6  6  4  4 34 A11  7  8  5 6  6  6  7  7  5  5 73 A11  7  7  6 6  6  6  8  8  6  6

TABLE 48 A9 System GZ7: sequence aligment mismach evaluatior forward primer reverse primer SEQ ID 227 228 229 230 256 257 258 259 260 261 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

21f1az 21f2bz 21f3dz 21f4cz 2r7C 2r8 2r10 2r12 2r12B 2r15 51 A5 4 4  3 4  8 11 11  8 12  9 26 A5 3 3  5 2 14 12 12 13 17 13 69 A5 4 4  4 4 14 11 11 13 17 14 82 A5 6 6  4 6  8 10  8  9 12  9 56 A6 5 5  4 4 14  8  7 13 14 16 30 A6 6 4  2 5 13  9 10 12 14 13 53 A6 6 4  4 7 12 10 10  9 12 14 66 A6 3 3  3 4 14  6  6 13 14 16 18 A7 6 6  5 6 13  8  8 11 13 15 39 A7 6 6  5 6 13 10  8 10 13 15 45 A7 7 7  6 7 12 11 10 10 11 14 59 A7 9 8  6 9 13  8  8 13 14 14 68 A7 13 10  8 10 13 15 85 A7 5 3  5 4  9 10  7 11 11 10 70 A7 6 6  4 6 10  7  7 10 11 12 16 A9 0 2  5 3  2 11  9  6  6  0 16 A9 0 2  5 3  2 11  9  6  6  0 31 A9 3 1  5 5  5 13 10  0  2  8 33 A9 4 4  0 4  8  0  2 10 11  9 35 A9 2 0  4 5  3 12 10  4  2  6 52 A9 2 4  6 0 12  6  3 11 14 15 58 A9 4 4  2 3 10  1  3 12 12 11 67 A9 3 5  3 2 13  5  7 14 14 14 54 A 4 4  5 5 12 11 12  9 13 13 42 A1 7 8  6 6 13 12 12 13 14 12 32 A1 6 7  7 5 14 12 12 15 15 13 61 A3 4 2  6 3 12 12 10 12 13 13 72 A3 5 4  3 5 14 13 11 13 14 13 89 A3 7 6  8 8 17 13 10 16 18 18 86 A3 8 9  7 7 14 15 12 13 15 14 87 A3 8 8  6 6 16 17 14 15 16 15 84 A3 8 8  5 7 16 15 12 15 17 14 83 A3 7 5  6 6 14 14 11 14 16 15 71 A3 7 6  8 8 14 18 15 11 14 15 90 A3 8 6 10 7 17 15 12 15 16 16 57 A4 7 7  8 7 14 14 11 14 15 16 57 A4 6 6  9 6 14 14 11 14 15 16  7 A8 5 6  9 5 12 10  9 15 15 12 40 A8 6 6  6 7 16 11  9 14 17 15 91 A8 5 5  9 8  9 12 11 11 11  9  6 A10 6 8  5 6 12 10 10 14 16 12  6 A10 6 8  5 6 13 10 10 15 17 13  6 A10 7 8  5 7 13 12 12 14 16 13 11 A10 6 7  7 5 14 12 12 16 16 14 44 A10 3 5  7 4 12 11 11 11 12 12 55 A10 4 6  7 3 11 11 11 10 11 11 74 A10 6 6  6 5 14 14 12 14 14 13 13 A10 6 8  6 6 12 12 12 11 15 12 34 A11 6 6  5 6  7 10  9  4  7  7 73 A11 7 6  4 7  9 10  9  8  9  9 A9 System GZ7: sequence aligment mismach evaluation probes SEQ ID 296 297 298 299 300 301 302 303 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

2Z7S1 2Z7S2 2Z7S2a 2Z7S2b 2Z7S3 2Z7S3a 2Z7S4 2Z7S4a 51 A5 5 5 5 5  9  9  6  6 26 A5 4 3 3 3  6  6  4  4 69 A5 2 3 3 3  7  7  3  3 82 A5 2 3 3 3  7  7  3  3 56 A6 7 7 7 7  9  9  7  7 30 A6 5 6 6 6  9  9  7  7 53 A6 7 5 5 5 10 10  8  8 66 A6 8 8 8 8 10 10  8  8 18 A7 6 1 1 1  8  8  6  6 39 A7 7 4 4 3  8  8  6  6 45 A7 5 3 3 3 10 10  6  6 59 A7 5 3 3 3  7  7  5  5 68 A7 85 A7 6 6 6 5 10 10  5  5 70 A7 7 5 5 4  8  8  6  6 16 A9 0 6 6 6  8  8  4  4 16 A9 1 5 5 5  9  9  5  5 31 A9 1 4 4 4  6  6  1  1 33 A9 5 1 1 1  9  9  7  7 35 A9 7 8 8 8  0  0  6  6 52 A9 4 3 3 3  7  7  2  2 58 A9 4 1 1 1  7  7  5  5 67 A9 4 1 1 1  7  7  4  4 54 A 5 8 8 8  8  8  5  5 42 A1 4 6 6 6  8  8  4  4 32 A1 5 6 6 6  9  9  5  5 61 A3 5 6 6 6  7  7  5  5 72 A3 4 8 8 8  7  7  5  5 89 A3 5 6 6 6  8  8  7  7 86 A3 6 9 9 9  8  8  9  9 87 A3 6 8 8 8  7  7  8  8 84 A3 7 9 9 9  8  8 10 10 83 A3 6 8 8 8  9  9  8  8 71 A3 6 7 7 7  9  9  7  7 90 A3 8 8 8 8  9  9  9  9 57 A4 7 6 6 6  9  9  8  8 57 A4 7 6 6 6  9  9  8  8  7 A8 9 9 9 9  3  3  8  8 40 A8 9 9 9 9  4  4  9  9 91 A8 4 5 5 5  3  3  5  5  6 A10 7 7 7 7 11 11  8  8  6 A10 7 7 7 7 11 11  8  8  6 A10 7 7 7 7 11 11  8  8 11 A10 6 9 9 9 10 10  8  8 44 A10 5 9 9 9  7  7  8  8 55 A10 5 9 9 9  7  7  8  8 74 A10 4 7 7 7  8  8  6  6 13 A10 3 7 7 7  6  6  4  4 34 A11 5 6 6 6  7  7  5  5 73 A11 6 6 6 6  8  8  6  6

TABLE 49 A9 System GZ8: sequence aligment mismach evaluation forward primer reverse primer SEQ ID 227 228 229 230 256 257 258 259 264 261 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

21f1az 21f2bz 21f3dz 21f4cz 2r7C 2r8 2r10 2r12 2r12B 2r15 51 A5 4 4  3 4  8 11 11  8 12  9 26 A5 3 3  5 2 14 12 12 13 17 13 69 A5 4 4  4 4 14 11 11 13 17 14 82 A5 6 6  4 6  8 10  8  9 12  9 56 A6 5 5  4 4 14  8  7 13 14 16 30 A6 6 4  2 5 13  9 10 12 14 13 53 A6 6 4  4 7 12 10 10  9 12 14 66 A6 3 3  3 4 14  6  6 13 14 16 18 A7 6 6  5 6 13  8  8 11 13 15 39 A7 6 6  5 6 13 10  8 10 13 15 45 A7 7 7  6 7 12 11 10 10 11 14 59 A7 9 8  6 9 13  8  8 13 14 14 68 A7 13 10  8 10 13 15 85 A7 5 3  5 4  9 10  7 11 11 10 70 A7 6 6  4 6 10  7  7 10 11 12 16 A9 0 2  5 3  2 11  9  6  6  0 16 A9 0 2  5 3  2 11  9  6  6  0 31 A9 3 1  5 5  5  3 10  0  2  8 33 A9 4 4  0 4  8  0  2 10 11  9 35 A9 2 0  4 5  3 12 10  4  2  6 52 A9 2 4  6 0 12  6  3 11 14 15 58 A9 4 4  2 3 10  1  3 12 12 11 67 A9 3 5  3 2 13  5  7 14 14 14 54 A 4 4  5 5 12 11 12  9 13 13 42 A1 7 8  6 6 13 12 12 13 14 12 32 A1 6 7  7 5 14 12 12 15 15 13 61 A3 4 2  6 3 12 12 10 12 13 13 72 A3 5 4  3 5 14 13 11 13 14 13 89 A3 7 6  8 8 17 13 10 16 18 18 86 A3 8 9  7 7 14 15 12 13 15 14 87 A3 8 8  6 6 16 17 14 15 16 15 84 A3 8 8  5 7 16 15 12 15 17 14 83 A3 7 5  6 6 14 14 11 14 16 15 71 A3 7 6  8 8 14 18 15 11 14 15 90 A3 8 6 10 7 17 15 12 15 16 16 57 A4 7 7  8 7 14 14 11 14 15 16 57 A4 6 6  9 6 14 14 11 14 15 16  7 A8 5 6  9 5 12 10  9 15 15 12 40 A8 6 6  6 7 16 11  9 14 17 15 91 A8 5 5  9 8  9 12 11 11 11  9  6 A10 6 8  5 6 12 10 10 14 16 12  6 A10 6 8  5 6 13 10 10 15 17 13  6 A10 7 8  5 7 13 12 12 14 16 13 11 A10 6 7  7 5 14 12 12 16 16 14 44 A10 3 5  7 4 12 11 11 11 12 12 55 A10 4 6  7 3 11 11 11 10 11 11 74 A10 6 6  6 5 14 14 12 14 14 13 13 A10 6 8  6 6 12 12 12 11 15 12 34 A11 6 6  5 6  7 10  9  4  7  7 73 A11 7 6  4 7  9 10  9  8  9  9 probes SEQ ID 304 305 306 307 308 309 310 311 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

2Z8S2f 2Z8S21f 2Z8S28f 2Z8S56f 2Z8S58f 2Z8S61f 2Z8S101f 2Z8S105f 51 A5  6  6  6 12 12 12 10 10 26 A5  8  8  8  9  9  9 14 14 69 A5  4  4  4 12 12 12 13 13 82 A5  6  6  6 12 12 12  8  8 56 A6  9  9  9 11 11 11 12 12 30 A6 10 10 10 13 13 13 15 15 53 A6  9  9  9 12 12 12 10 10 66 A6  8  8  8 10 10 10 12 12 18 A7  8  8  8 10 10 10 12 12 39 A7  9  9  9 13 13 13 11 11 45 A7  8  8  8 11 11 11 13 13 59 A7  9  9  9  9  9  9 13 13 68 A7 85 A7  9  9  9 10 10 10  9  9 70 A7  8  8  8 11 11 11  9  9 16 A9  0  0  0 10 10 10 12 12 16 A9  1  1  1 11 11 11 12 12 31 A9  9  9  9  0  0  0 13 13 33 A9  8  8  8 13 13 13  0  0 35 A9  9  9  9 10 10 10 11 11 52 A9  8  8  8 12 12 12 12 12 58 A9 10 10 10 11 11 11  7  7 67 A9  7  7  7 10 10 10  9  9 54 A  9  9  9 10 10 10 12 12 42 A1  9  9  9 12 12 12 13 13 32 A1  7  7  7 12 12 12 10 10 61 A3  9  9  9 12 12 12 11 11 72 A3 13 13 13 14 14 14 15 15 89 A3  9  9  9 12 12 12 14 14 86 A3 13 13 13 12 12 12 13 13 87 A3 13 13 13 13 13 13 15 15 84 A3 10 10 10 10 10 10 12 12 83 A3  7  7  7 11 11 11 11 11 71 A3  8  8  8 14 14 14 15 15 90 A3  8  8  8 12 12 12 14 14 57 A4  9  9  9 11 11 11 14 14 57 A4  9  9  9 12 12 12 15 15  7 A8  9  9  9 13 13 13 12 12 40 A8  8  8  8 12 12 12 12 12 91 A8  7  7  7 10 10 10 12 12  6 A10  8  8  8 12 12 12 11 11  6 A10  8  8  8 12 12 12 11 11  6 A10  7  7  7 12 12 12 11 11 11 A10  8  8  8 12 12 12 12 12 44 A10  7  7  7 14 14 14  8  8 55 A10  4  4  4 12 12 12  9  9 74 A10  8  8  8 13 13 13  8  8 13 A10  9  9  9  8  8  8  7  7 34 A11 10 10 10  9  9  9 12 12 73 A11  9  9  9 11 11 11  7  7 probes SEQ ID 312 313 314 315 316 317 318 319 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

2Z8S127f 2Z8S146f 2Z8S155f 2Z8S156f 2Z8S210f 2Z8S231f 2Z8S236f 2Z8S250f 51 A5 10 11 11 11 12 10 10 10 26 A5 14 14 14 14  9  9  9  9 69 A5 13 14 14 14  7  8  8  8 82 A5  8 14 14 14 12  9  9  9 56 A6 12 15 15 15  5  7  7  7 30 A6 15 15 15 15  8 11 11 11 53 A6 10 12 12 12  6  6  6  6 66 A6 12 12 12 12  5  7  7  7 18 A7 12 12 12 12  6  7  7  7 39 A7 11 10 10 10 10  6  6  6 45 A7 13 13 13 13  9 10 10 10 59 A7 13 10 10 10  7  6  6  6 68 A7 85 A7  9 10 10 10  8  5  5  5 70 A7  9 10 10 10  6  5  5  5 16 A9 12 12 12 12  9  9  9  9 16 A9 12 11 11 11  9  8  8  8 31 A9 13 12 12 12 10  9  9  9 33 A9  0 13 13 13 11  6  6  6 35 A9 11  0  0  0 10  9  9  9 52 A9 12 13 13 13  0  5  5  5 58 A9  7 11 11 11  6  0  0  0 67 A9  9 14 14 14  7  3  3  3 54 A 12 11 11 11  8  8  8  8 42 A1 13 14 14 14  7  9  9  9 32 A1 10 12 12 12  9  9  9  9 61 A3 11 15 15 15  9  8  8  8 72 A3 15 17 17 17 11 13 13 13 89 A3 14 13 13 13 10 10 10 10 86 A3 13 17 17 17  8 10 10 10 87 A3 15 16 16 16  9 11 11 11 84 A3 12 16 16 16 12 10 10 10 83 A3 11 12 12 12 13 10 10 10 71 A3 15 15 15 15 12 11 11 11 90 A3 14 14 14 14 12 12 12 12 57 A4 14 13 13 13 10 11 11 11 57 A4 15 14 14 14 10 12 12 12  7 A8 12 13 13 13  8 10 10 10 40 A8 12 13 13 13  8 12 12 12 91 A8 12 12 12 12 10 11 11 11  6 A10 11 13 13 13 10  8  8  8  6 A10 11 13 13 13 10  8  8  8  6 A10 11 13 13 13 10  8  8  8 11 A10 12 13 13 13  8  8  8  8 44 A10  8 15 15 15  7  9  9  9 55 A10  9 13 13 13  8  9  9  9 74 A10  8 14 14 14  8  6  6  6 13 A10  7 12 12 12  9  6  6  6 34 A11 12 15 15 15 12  9  9  9 73 A11  7 12 12 12 11  6  6  6

TABLE 50 A9 System H forward primer SEQ ID 232 232 233 234 235 236 237 238 239 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

2f5 2f6 2f7 2f8 2f9 2f10 2f10b 2f11 2f12 51 A5 4  8  8 5  6  4  5  5  6 26 A5 3  7  8 4  3  3  4  3  4 69 A5 2  8  6 2  3  2  3  3  4 82 A5 2  6  4 2  3  2  3  3  4 56 A6 6 10 11 7  6  5  6  8  7 30 A6 3 10 11 5  4  5  5  7  6 53 A6 6 12 13 7  7  4  5  6  7 66 A6 7 10 11 8  7  6  7  9  8 18 A7 4  7  8 6  3  2  2  4  5 39 A7 5  7  9 6  3  4  4  4  5 45 A7 4 10  9 5  5  3  3  5  6 59 A7 3  7  9 5  3  4  4  3  4 68 A7 5  7  9 6  3  4  4  4  5 85 A7 5  9  8 5  4  4  4  6  6 70 A7 5  6  8 6  3  4  4  5  5 16 A9 0  8  6 0  4  2  3  5  4 16 A9 1  8  6 1  5  1  2  6  5 31 A9 1  5  3 1  2  1  2  4  3 33 A9 3 10 10 5  3  1  1  4  5 35 A9 5  0  2 7  6  6  7  2  2 52 A9 3  8  8 4  3  3  3  2  3 58 A9 2  9  9 4  1  0  0  5  4 67 A9 2  8  8 4  1  0  0  5  4 54 A 4  7  6 4  6  4  5  7  7 42 A1 3  7  6 3  4  3  3  6  5 32 A1 5  9  7 5  6  3  4  8  7 61 A3 4  7  6 4  5  2  3  6  6 72 A3 3  7  6 3  5  4  5  6  6 89 A3 3  7  7 4  5  2  3  7  7 86 A3 5  9  8 6 10  6  7  6  7 87 A3 5  9  8 6  9  6  7  6  7 84 A3 5  9  9 7 10  6  7  6  7 83 A3 4 10 10 6  8  4  5  7  7 71 A3 5 10  9 5  7  4  5  7  8 90 A3 8 12 11 7  9  6  7  7  8 57 A4 5 10 10 6  7  4  5  6  8 57 A4 5 10 10 6  7  4  5  6  8  7 A8 6  5  7 9  7  7  8  3  3 40 A8 6  8  9 9  7  7  8  4  4 91 A8 3  5  5 4  3  3  4  4  3  6 A10 6 11 10 6  6  4  4  7  7  6 A10 6 11 10 6  6  4  4  7  7  6 A10 6 11 10 6  6  4  4  7  7 11 A10 5  9  8 5  8  5  6  7  8 44 A10 4  8  7 5  9  5  6  6  6 55 A10 4  8  7 5  9  5  6  6  6 74 A10 3 10  9 4  7  3  4  6  6 13 A10 2  8  7 3  5  3  4  4  4 34 A11 4  8  9 5  4  4  5  6  5 73 A11 5  8  9 6  5  4  5  7  6 reverse primer SEQ ID 262 257 263 258 259 256 264 261 265 NO:  

A9E A9E A9E A9E A9E A9E A9E A9E A9E N^(o)HPV Group 

2r7B 2r8 2r9 2r10 2r12 2r7C 2r12B 2r15 2r16 51 A5  8 11 10 11  8  8 12  9 14 26 A5 13 12 11 12 13 14 17 13 15 69 A5 14 11 10 11 13 14 17 14 13 82 A5  8 10  8  8  9  8 12  9 12 56 A6 13  8  7  7 13 14 14 16 10 30 A6 13  9  9 10 12 13 14 13 11 53 A6 12 10  9 10  9 12 12 14 14 66 A6 13  6  5  6 13 14 14 16 11 18 A7 12  8  8  8 11 13 13 15 10 39 A7 12 10  8  8 10 13 13 15 12 45 A7 11 11 11 10 10 12 11 14 10 59 A7 13  8  9  8 13 13 14 14  8 68 A7 12 10  8  8 10 13 13 15 12 85 A7  9 10  8  7 11  9 11 10 10 70 A7 10  7  6  7 10 10 11 12 11 16 A9  2 11 10  9  6  2  6  0 10 16 A9  2 11 10  9  6  2  6  0 10 31 A9  5 13 11 10  0  5  2  8 11 33 A9  9  0  1  2 10  8 11  9  2 35 A9  3 12 11 10  4  3  2  6 11 52 A9 12  6  4  3 11 12 14 15  8 58 A9 11  1  2  3 12 10 12 11  0 67 A9 13  5  6  7 14 13 14 14  5 54 A 12 11 11 12  9 12 13 13 15 42 A1 13 12 12 12 13 13 14 12 13 32 A1 13 12 11 12 15 14 15 13 13 61 A3 12 12 11 10 12 12 13 13 12 72 A3 14 13 12 11 13 14 14 13 12 89 A3 17 13 11 10 16 17 18 18 14 86 A3 14 15 13 12 13 14 15 14 16 87 A3 15 17 15 14 15 16 16 15 18 84 A3 15 15 13 12 15 16 17 14 15 83 A3 14 14 12 11 14 14 16 15 15 71 A3 14 18 16 15 11 14 14 15 17 90 A3 15 15 13 12 15 17 16 16 16 57 A4 13 14 12 11 14 14 15 16 14 57 A4 13 14 12 11 14 14 15 16 14  7 A8 11 10 10  9 15 12 15 12 11 40 A8 15 11 10  9 14 16 17 15 12 91 A8  9 12 12 11 11  9 11  9 13  6 A10 13 10  9 10 14 12 16 12 14  6 A10 14 10  9 10 15 13 17 13 15  6 A10 14 12 11 12 14 13 16 13 16 11 A10 15 12 11 12 16 14 16 14 15 44 A10 11 11 10 11 11 12 12 12 14 55 A10 10 11 10 11 10 11 11 11 13 74 A10 13 14 13 12 14 14 14 13 16 13 A10 12 12 11 12 11 12 15 12 14 34 A11  6 10  8  9  4  7  7  7 13 73 A11  7 10  8  9  8  9  9  9 12 probes 304 305 306 307 308 309 310 311 SEQ ID A9E A9E A9E A9E A9E A9E A9E A9E NO:  

2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S NoHPV Group 

2f 21f 28f 56f 58f 61f 101f 105f 51 A5  6  6  6 12 12 12 10 10 26 A5  8  8  8  9  9  9 14 14 69 A5  4  4  4 12 12 12 13 13 82 A5  6  6  6 12 12 12  8  8 56 A6  9  9  9 11 11 11 12 12 30 A6 10 10 10 13 13 13 15 15 53 A6  9  9  9 12 12 12 10 10 66 A6  8  8  8 10 10 10 12 12 18 A7  8  8  8 10 10 10 12 12 39 A7  9  9  9 13 13 13 11 11 45 A7  8  8  8 11 11 11 13 13 59 A7  9  9  9  9  9  9 13 13 68 A7 85 A7  9  9  9 10 10 10  9  9 70 A7  8  8  8 11 11 11  9  9 16 A9  0  0  0 10 10 10 12 12 16 A9  1  1  1 11 11 11 12 12 31 A9  9  9  9  0  0  0 13 13 33 A9  8  8  8 13 13 13  0  0 35 A9  9  9  9 10 10 10 11 11 52 A9  8  8  8 12 12 12 12 12 58 A9 10 10 10 11 11 11  7  7 67 A9  7  7  7 10 10 10  9  9 54 A  9  9  9 10 10 10 12 12 42 A1  9  9  9 12 12 12 13 13 32 A1  7  7  7 12 12 12 10 10 61 A3  9  9  9 12 12 12 11 11 72 A3 13 13 13 14 14 14 15 15 89 A3  9  9  9 12 12 12 14 14 86 A3 13 13 13 12 12 12 13 13 87 A3 13 13 13 13 13 13 15 15 84 A3 10 10 10 10 10 10 12 12 83 A3  7  7  7 11 11 11 11 11 71 A3  8  8  8 14 14 14 15 15 90 A3  8  8  8 12 12 12 14 14 57 A4  9  9  9 11 11 11 14 14 57 A4  9  9  9 12 12 12 15 15  7 A8  9  9  9 13 13 13 12 12 40 A8  8  8  8 12 12 12 12 12 91 A8  7  7  7 10 10 10 12 12  6 A10  8  8  8 12 12 12 11 11  6 A10  8  8  8 12 12 12 11 11  6 A10  7  7  7 12 12 12 11 11 11 A10  8  8  8 12 12 12 12 12 44 A10  7  7  7 14 14 14  8  8 55 A10  4  4  4 12 12 12  9  9 74 A10  8  8  8 13 13 13  8  8 13 A10  9  9  9  8  8  8  7  7 34 A11 10 10 10  9  9  9 12 12 73 A11  9  9  9 11 11 11  7  7 probes 312 313 314 315 316 317 318 319 SEQ ID A9E A9E A9E A9E A9E A9E A9E A9E NO:  

2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S 2Z8S N^(o)HPV Group 

127f 146f 155f 156f 210f 231f 236f 250f 51 A5 10 11 11 11 12 10 10 10 26 A5 14 14 14 14  9  9  9  9 69 A5 13 14 14 14  7  8  8  8 82 A5  8 14 14 14 12  9  9  9 56 A6 12 15 15 15  5  7  7  7 30 A6 15 15 15 15  8 11 11 11 53 A6 10 12 12 12  6  6  6  6 66 A6 12 12 12 12  5  7  7  7 18 A7 12 12 12 12  6  7  7  7 39 A7 11 10 10 10 10  6  6  6 45 A7 13 13 13 13  9 10 10 10 59 A7 13 10 10 10  7  6  6  6 68 A7 85 A7  9 10 10 10  8  5  5  5 70 A7  9 10 10 10  6  5  5  5 16 A9 12 12 12 12  9  9  9  9 16 A9 12 11 11 11  9  8  8  8 31 A9 13 12 12 12 10  9  9  9 33 A9  0 13 13 13 11  6  6  6 35 A9 11  0  0  0 10  9  9  9 52 A9 12 13 13 13  0  5  5  5 58 A9  7 11 11 11  6  0  0  0 67 A9  9 14 14 14  7  3  3  3 54 A 12 11 11 11  8  8  8  8 42 A1 13 14 14 14  7  9  9  9 32 A1 10 12 12 12  9  9  9  9 61 A3 11 15 15 15  9  8  8  8 72 A3 15 17 17 17 11 13 13 13 89 A3 14 13 13 13 10 10 10 10 86 A3 13 17 17 17  8 10 10 10 87 A3 15 16 16 16  9 11 11 11 84 A3 12 16 16 16 12 10 10 10 83 A3 11 12 12 12 13 10 10 10 71 A3 15 15 15 15 12 11 11 11 90 A3 14 14 14 14 12 12 12 12 57 A4 14 13 13 13 10 11 11 11 57 A4 15 14 14 14 10 12 12 12  7 A8 12 13 13 13  8 10 10 10 40 A8 12 13 13 13  8 12 12 12 91 A8 12 12 12 12 10 11 11 11  6 A10 11 13 13 13 10  8  8  8  6 A10 11 13 13 13 10  8  8  8  6 A10 11 13 13 13 10  8  8  8 11 A10 12 13 13 13  8  8  8  8 44 A10  8 15 15 15  7  9  9  9 55 A10  9 13 13 13  8  9  9  9 74 A10  8 14 14 14  8  6  6  6 13 A10  7 12 12 12  9  6  6  6 34 A11 12 15 15 15 12  9  9  9 73 A11  7 12 12 12 11  6  6  6

TABLE 51 list of HPV plasmids Name Group Plasmid size kb Insert size kb Source Publications pHPV 16 A9 2.961 7.904 ATCC 45113 pHPV 6B A10 2.686 7.900 ATCC 45150 The EMBO Journal vol2 n^(o)12 p.2341-2348 (1983) pHPV 18 A7 4.363 7.857 ATCC 45152 J. Mol. Biol, (1987) 193 p.599-608 pHPV 31 A9 4.363 8.000 ATCC 65446 J Virol 58: 225-229, 1986 pHPV 11 A10 4.363 7.931 ATCC 45151 Virology 151 124-130 (1986) pHPV 35 cl 2A A9 4.363 3.750 ATCC 40330 U.S. Pat. No. 4,849,332 pHPV 35 cl 2B A9 4.363 4.100 ATCC 40331 U.S. Pat. No. 4,849,332 pHPV 56 cl 2A A6 2.818 5.100 ATCC 40341 U.S. Pat. No. 4,908,306 pHPV 56 cl 2C A6 2.818 7.900 ATCC 40549 U.S. Pat. No. 4,908,306 pHPV 56 cl 2B A6 2.818 3.100 ATCC 40379 U.S. Pat. No. 4,908,306 pHPV 43 cl 2A A8 2.812 6.300 ATCC 40338 U.S. Pat. No. 4,849,334 pHPV 43 cl 2B A8 2.812 2.850 ATCC 40339 U.S. Pat. No. 4,849,334 pHPV 44 cl 2 A10 2.818 7.800 ATCC 40353 U.S. Pat. No. 4,849,331 pHPV 7cl 7/4 A8 2.686 3.905 DKFZ pHPV 7cl 7/5 A8 2.686 4.131 DKFZ pHPV 13 cl 13 A10 2.686 7.241 DKFZ pHPV 30 cl 30 A6 4.36 7.157 DKFZ pHPV 40 cl 40 A8 2.686 7.296 DKFZ pHPV 53 cl 53 A8 3.939 7.154 DKFZ pHPV 57 cl 57 A4 2.686 7.235 DKFZ pHPV 72 cl 72 A3 2.961 7.307 DKFZ pHPV 73 cl 73 A11 2.961 7.005 DKFZ pHPV 45 cl 45 A7 2.871 7.149 DKFZ pHPV 51 A5 2.68 7.800 DKFZ J. of Virology 1998 p1452-1455/aug.1991 p.4216-4225 pHPV 26 A5 2.686 7.100 DKFZ pHPV 52 A9 2.686 7.940 DKFZ pHPV 89 Frag 1 A3 3.015 0.700 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 89 Frag 2 A3 3.015 1.100 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 89 Frag 3 A3 3.015 2000 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 89 Frag 4 A3 3.015 5.100 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 62 Frag 1 A3 3.015 3.325 DKFZ pHPV 62 Frag 2 A3 3.015 4.040 DKFZ pHPV 62 Frag 3 A3 3.015 1.268 DKFZ pHPV 84 Frag 1 A3 3.015 0.700 DKFZ Virology 279, 109-115, 2001 pHPV 84 Frag 2 A3 3.015 4.500 DKFZ Virology 279, 109-115, 2001 pHPV 84 Frag 3 A3 3.015 1000 DKFZ Virology 279, 109-115, 2001 pHPV 84 Frag 4 A3 3.015 1.800 DKFZ Virology 279, 109-115, 2001 pHPV 84 Frag 5 A3 3.015 0.600 DKFZ Virology 279, 109-115, 2001 pHPV 90 Frag1 A3 3.015 4.200 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 90 Frag 2 A3 3.015 1.700 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 90 Frag 3 A3 3.015 2.500 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 86 Frag 1 A3 3.015 3.900 DKFZ J Gen Virol 2001, 82, 2035-2040 pHPV 86 Frag 2 A3 3.015 5.800 DKFZ J Gen Virol 2001, 82, 2035-2040 pHPV 86 Frag 3 A3 3.015 0.140 DKFZ J Gen Virol 2001, 82, 2035-2040 pHPV 91 Frag 1 A8 3.015 3.200 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 91 Frag 2 A8 3.015 1.500 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 91 Frag 3 A8 3.015 1.400 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 91 Frag 4 A8 3.015 2.500 DKFZ The Journal of infectious diseases 2002 185: 1794-7 pHPV 33 A9 4.363 7.093 CNCM I-450 pHPV 39 A7 3.005 7.160 CNCM I-507 JCM mar 1996, 738-744 pHPV 42 A1 3.030 7.107 CNCM I-508 pHPV 54 A4 3.030 7.107 CNCM I-756 pHPV 23 B1 4.363 7.324 CNCM I-391 J Virol, dec 1984, 52, 1013-1018 pHPV 68 A7 4.363 6.042 CNCM I-1540 JCM mar 1996, 738-744/U.S. Pat. No. 5,981,173 pHPV 66 A6 4.363 7.158 CNCM I-951 J virol, 1986, 57, 688-692 pHPV 87 L1 E1 16 A3 3.015 1.014 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 87 L1 f A3 3.015 0.974 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 87 MY 16 A3 3.015 0.448 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 87 E1 L1 11/2 A3 3.015 2.794 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 87 L1 E1 37 A3 3.015 1.227 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 87 E11 E2 as A3 3.015 1.130 DKFZ Journal of Virology dec.2001 p11913-11919 pHPV 58 A8 3.800 7.824 DKFZ Virology (1990) 177: 833-836 pHPV 59 AT 2.695 7.896 DKFZ Int. J. Cancer (1995) 61: 13-22 pHPV 67 A9 2.695 7.801 DKFZ Int. J. Cancer (1995) 61: 13-22 pHPV 81 A3 3.204 4.759 DKFZ Virology (2001) 283: 139-147 pHPV 82 A5 3.204 7.871 DKFZ Clin. Diagn. Lab. Immu. (2000) 7: 91-95 pHPV 85 A7 3.500 7.812 DKFZ Journal of General Virology (1999) 80, 2923-2929 DKFZ is Deusches Kresbsorschungszentrum; Tumorvirologie; ATV0660; Im Neuenheimer Feld 242; DE-Heidelberg; Germany; CNCM is Collection Nationale de Cultures de Microorganisme; Institut Pasteur; 25, rue du Docteur Roux; F-75724 Paris Cedex 15; France; ATCC is American Type Culture Collection; 10801 University Blvd.; Manassas, Virginia 20110-2209; U.S.A. All HPV strains are available from DKFZ.

TABLE 52 A5 and A6 Systems PCR simplex probe conditions Kit Kit Quantitect probe PCR MgCl₂ 6 mM Plasmid concentration 10⁸ cop de plasmides/PCR A5 System A. B. C. D. E: PCR simplex probe conditions forward primer reverse primer probes Thermoprofile Name μM Name μM Name μM System A 55° C. A5E6f1 0.4 A5E6r1 0.4 A5E6S1 0.3 System A 53° C. A5E6f1 0.4 A5E6r1 0.4 A5E6S1b 0.2 System B 55° C. A5E6f2 0.3 A5E6r2 0.3 A5E6S2 0.4 System C 55° C. A5E6f3 0.6 A5E6r3 0.6 A5E6S3 0.3 System D 56° C. A5E6f4 0.3 A5E6r4 0.3 A5E6S4 0.3 System E 55° C. A5E6f5 0.6 A5E6r5 0.6 A5E6S4 0.2 A6 System A . B. C. D. E: PCR simplex probe carditions forward primer reverse primer probes Thermoprofile Name μM Name μM Name μM System A 58° C. A6E6f1 0.4 A6E6r1 0.4 A6E6S1 0.3 System B 57° C. A6E6f2 0.6 A6E6r1 0.6 A6E6S1 0.4 System C 55° C. A6E6f3 0.6 A6E6r2 0.6 A6E6S2 0.3 System C 57° C. A6E6f3 0.6 A6E6r2 0.6 A6E6S2b 0.2 System D 58° C. A6E6f4 0.5 A6E6r1 0.5 A6E6S1 0.4 System E 57° C. A6E6f5 0.4 A6E6r3 0.4 A6E6S3 0.3 System E 56° C. A6E6f5 0.4 A6E6r3 0.4 A6E6S3b 0.2

TABLE 53 A5 System A, B, C, D, E, specificity Syt A Syt A Syt B Syt C Syt D Syt E A5E6S1b A5E6S1 A5E6S2 A5E6S3 A5E6S4 A5E6S4 N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 51 A5 22.2* 500 10.95 600  9.9 350 9.9 500 10.5 1200 9.6 1700 26 A5 ND ND ND ND ND ND ND ND ND ND ND ND 69 A5 NT NT NT NT NT NT NT NT NT NT NT NT 82 A5 ND ND ND ND 22.5 200 ND ND ND ND ND ND Other HPV ND ND ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND ND ND H2O sample ND ND ND ND ND ND ND ND ND ND ND ND *Plasmid concentration: 5.10⁵ copies of plasmids/PCR ND: no Detection NT: no test

TABLE 54 A6 System A, B, C, D, E, specificity Syt A Syt B Syt C Syt C Syt D Syt E Syt E A6E6S1 A6E6S1 A6E6S2 A6E6S2b A6E6S1 A5E6S3 A5E6S3b N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 56 A6 14.3 250 13.0 500 13.6 3200 19.9* 700 14.3 550 12.3  350 18.5* 900 30 A6 ND ND ND ND ND ND ND ND ND ND ND ND ND ND 53 A6 NT NT NT NT NT NT NT NT NT NT NT NT NT NT 66 A6 ND ND ND ND ND ND ND ND ND ND 22.6* 450 24.9* 820 Other HPV ND ND ND ND ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND H2O sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND *Plasmid concentration: 5 10⁶ copies of plasmids/PCR ND: no Detection NT: no test

TABLE 55 A7 System A. B. C. D: PCR simplex probe and PCR multiplex probes conditions Kit Kit Quantitect probe PCR MgCl₂ 6 mM Plasmid concentration 10⁶ cop de plasmides/PCR forward primer reverse primer probes Thermoprofile Name μM Name μM Name μM System A 53° C. A7E16f1a 0.3 A7E16r1b 0.2 A7E1ZAS61f 0.2 A7E16f2a 0.3 A7E16r2b 0.3 A7E1S63f 0.2 A7E16f3a 0.3 A7E16r3b 0.3 A7E1S64f 0.2 A7E1S40f 0.2 A7E1ZBS74f 0.2 System B 52° C. A7E115f1a 0.3 A7E115r1a 0.2 A7E1ZBS26f 0.2 A7E115f2a 0.3 A7E115r2b 0.3 A7E1ZBS74f 0.2 A7E115f3d 0.3 A7E1ZBS80f 0.2 System C 51° C. A7E17f1 0.4 A7E17r1 0.3 A7E1ZCS11f 0.2 A7E17f2 0.4 A7E17r2 0.4 A7E1ZCS45f 0.2 A7E17f3 0.4 A7E1ZCS63f 0.2 A7E1ZCS90f 0.2 System D 53° C. A7E12f1 0.3 A7E12r2 0.3 A7E1S36f 0.2 A7E12f2 0.3 A7E12r3 0.1 A7E1S37f 0.2 A7E1S38f 0.2 A7E1ZDS2f 0.2

TABLE 56 A7 System A. specificity Multiplex A7E1ZAS61f A7E1ZAS63f Simplex Simplex Simplex Simplex Simplex 7E1ZCS40f Probe A7E1ZAS61f A7E1ZAS63f A7E1ZAS64f A7E1ZCS40f A7E1ZBS74f A7E1ZBS74f N^(o) HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 18 A7 22.5 175 ND ND ND ND ND ND ND ND 22.5 168 39 A7 ND ND ND ND 22.1 145 ND ND 22.8 248 21.0 263 45 A7 ND ND ND ND ND ND 25.5 115 ND ND 20.3 160 59 AT ND ND 20.5 62.5 ND ND ND ND ND ND 20.2 188 68 A7 ND ND ND ND ND ND ND ND 26.2 125 25.9  31 85 A7 ND ND ND ND ND ND ND ND ND ND ND ND 70 A7 NT NT NT NT NT NT NT NT NT NT NT NT Other HPV ND ND ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND ND: no Detection NT: no test

TABLE 57 A7 System B. specificity Simplex Simplex Simplex Simplex Simplex Probe A7E1ZBS74f A7E1ZBS79f A7E1ZB80f A7EIZBS26f A7EIZBS27f N^(o)HPV Groupe CT RFU CT RFU CT RFU CT RFU CT RFU 18 A7 ND ND ND ND ND ND 22.9 770 22.5  43 39 A7 24.2 900 ND ND ND ND ND ND ND ND 45 A7 ND ND ND ND ND ND 25.6 312 21.7 665 59 A7 ND ND 18.6 2525 21.2 845 ND ND ND ND 68 A7 25.7  77 ND ND ND ND ND ND ND ND 85 A7 ND ND ND ND ND ND ND ND ND ND 70 A7 NT NT NT NT NT NT NT NT NT NT Other HPV ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND Multiplex Multiplex Multiplex A7E1ZBS26f A7E1ZBS26f A7E1ZBS26f A7E1ZBS74f A7E1ZBS74f A7E1ZBS74f A7E1ZBS80f Probe A7E1ZBS79f A7E1ZBS80f A7E1ZBS27f N^(o)HPV Groupe CT RFU CT RFU CT RFU 18 A7 22.3 215 20.9 248 20.3 318 39 A7 34.8 155 26.7 375 32.9 213 45 A7 26 72 26.3  98 26.2 173 59 A7 24 505 21.7 338 21.5 308 68 A7 34.5 128 22.8 163 27.1 135 85 A7 ND ND ND ND ND ND 70 A7 NT NT NT NT NT NT DNA sample ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND: no Detection NT: no test

TABLE 58 A7 System C. specificity Multiplex Multiplex A7E1ZCS40f A7E1ZCS11f A7E1ZCS45f A7E1ZCS45f Simplex Simplex Simplex Simplex Simplex A7E1ZCS63f 7E1ZCS63f Probe A7E1ZCS11f A7E1ZCS40f A7E1ZCS45f A7E1ZCS63f A7E1ZCS90f A7E1ZCS90f A7E1ZCS90f N^(o)HPV Groupe CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 18 A7 22.0 247 23.4 200 ND ND ND ND ND ND 22.6 231 22.0 239 39 A7 ND ND ND ND 21.9 350 ND ND ND ND 21.7 649 21.1 451 45 A7 21.9 349 24.0 325 ND ND ND ND ND ND 25.6 319 24.7 192 59 A7 ND ND 24.4 35 ND ND 22.4 400 ND ND 24.4 491 25.3 309 68 A7 ND ND ND ND ND ND ND ND 26.2 250 24.5 344 25.3 181 85 A7 ND ND ND ND ND ND ND ND ND ND ND ND ND ND 70 A7 NT NT NT NT NT NT NT NT NT NT NT NT NT NT Other HPV ND ND ND ND ND ND ND ND ND ND NT NT NT NT DNA sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND: no Detection NT: no test

TABLE 59 A7 System D. specificity Multiplex Multiplex A7E1S36f A7E1S3f A7E1S37f A7E1S37f Simplex Simplex Simplex Simplex Simplex A7E1S38f A7E1S38f Probe A7E1ZDS37f A7E1ZDS38f A7E1S36 f A7E1ZDS2f A7E1ZDS3f A7E1ZDS2f A7E1ZDS2f N^(o)HPV Groupe CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 18 A7 23.0 230 ND ND ND ND ND ND ND ND 21.1 357 21.8 420 39 A7 ND ND 23.9 269 ND ND 25.1 323 ND ND 22.5 233 22.3 310 45 A7 ND ND ND ND 27.2 426 ND ND 23.0 1545 26.6 295 23.5 508 59 A7 ND ND 23.8 592 ND ND ND ND ND ND 22.6 135 22.6 230 68 A7 ND ND ND ND ND ND 22.9 897 ND ND 23.4 363 23.5 548 85 A7 ND ND 31.8 262 ND ND ND ND ND ND 32.6  63 29.2 103 70 A7 NT NT NT NT NT NT NT NT NT NT NT NT NT NT Other HPV ND ND ND ND ND ND ND ND ND ND NT NT NT NT DNA sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND: no Detection NT: no test

TABLE 60 A9 Systems: PCR simplex and PCR multiplex probes conditions Kit Kit Quantitect probe PCR MgCl₂ 5 mM Plasmid concentration 10⁶ cop/PCR forward primer reverse primer probes Thermoprofile Name μM Name μM Name μM System C 51° C. A9E1f8 0.4 A9E1r5 0.4 A9E1S10a 0.2 A9E1f10 0.4 A9E1r6 0.4 A9E1S12a 0.2 A9E1f12 0.2 System E2 52° C. A9E2f1a 0.4 A9E2r1 0.4 A9E2Z7S1 0.2 A9E2f2a 0.6 A9E2r2 0.4 A9E2Z7S2 0.2 A9E2f4a 0.4 A9E2r4 0.6 A9E2Z7S3a 0.2 A9E2r13 0.4 A9E2Z7S4a 0.2 A9E2r14 0.4 System E3 52° C. A9E2f1a 0.4 A9E21r1cz 0.4 A9E2Z7S1 0.2 A9E2f2a 0.4 A9E21r2az 0.4 A9E2Z7S2 0.2 A9E2f4a 0.4 A9E21r3az 0.4 A9E2Z7S3a 0.2 A9E21r4fz A9E2Z7S4a 0.2 A9E21r5az System E4 52° C. A9E2Z5Z6f1c 0.4 A9E21r1cz 0.4 A9E2Z7S1 0.2 A9E2Z5Z6f2c 0.4 A9E21r2az 0.4 A9E2Z7S2 0.2 A9E2Z5Z6f3b 0.4 A9E21r3az 0.4 A9E2Z7S3a 0.2 A9E21r4fz A9E2Z7S4a 0.2 A9E21r5az System F 52° C. A9E2-1f1az 0.4 A9E2-1r1cz 0.4 A9E2Z7S1 0.2 A9E2-1f2bz 0.5 A9E2-1r2az 0.4 A9E2Z7S2 0.2 A9E2-1f3dz 0.4 A9E2-1r3az 0.4 A9E2Z7S3a 0.2 A9E2-1f4cz 0.4 A9E2-1r4fz 0.4 A9E2Z7S4a 0.2 A9E2-1r5az 0.4 System G Z7 52° C. A9E2-1f1az 0.4 A9E2r8 0.4 A9E2Z7S1 0.2 A9E2-1f2bz 0.4 A9E2r10 0.4 A9E2Z7S2a 0.2 A9E2-1f3dz 0.4 A9E2r12 0.4 A9E2Z7S3a 0.2 A9E2-1f4cz 0.5 A9E2r12B 0.4 A9E2Z7S4a 0.2 A9E2r15 0.4 System G Z8 52° C. A9E2-1f1az 0.6 A9E2r8 0.4 A9E2Z8S2f 0.2 A9E2-1f2bz 0.4 A9E2r10 0.4 A9E2Z8S61f 0.2 A9E2-1f3dz 0.4 A9E2r12 0.4 A9E2Z8S127f 0.2 A9E2-1f4cz 0.5 A9E2r12B 0.4 A9E2Z8S156f 0.2 A9E2r15 0.6 A9E2Z8S210f 0.2 A9E2Z8S250f 0.2 System H 53° C. A9E2f6 0.4 A9E2r10 0.4 A9E2Z8S2f 0.2 A9E2f8 0.4 A9E2r12B 0.4 A9E2Z8S61f 0.2 A9E2f9 0.4 A9E2r15 0.4 A9E2Z8S127f 0.2 A9E2r16 0.4 A9E2Z8S156f 0.2 A9E2Z8S210f 0.2 A9E2Z8S231f 0.2 A9E2Z8S250f 0.2

TABLE 61 A9 System C specificity Multiplex Simplex Simplex Simplex Simplex Simplex Simplex Simplex A9E2S10a Probes A9E1S10* A9E1S10a A9E1S11* A9E1S11a* A9E1S12* A9E1S12a A9E1S12b* A9E2S12a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 22.3 1125 21.9 492 NT NT NT NT NT NT ND ND NT NT 21.0 442 31 A9 27.3 625 23.0 469 25.7 679 24.6 415 39.4 14.5 26.6 103 ND ND 20.8 458 33 A9 25.8 450 22.9 374 NT NT NT NT NT NT ND ND NT NT 22.3 327 35 A9 33.0 181 24.9 188 27.2 342 26.4 234 26.5 224 23.2 502 26.9 241 23.0 435 52 A9 23.4 1059 22.7 599 NT NT 23.8 215 NT NT ND ND NT NT 21.7 581 58 A9 23.5 1435 23.7 582 NT NT 24.3 278 NT NT ND ND NT NT 23.7 525 67 A9 25.0 334 22.4 294 NT NT NT NT NT NT ND ND NT NT 21.9 279 53 A6 NT NT 29.7 449 NT NT NT NT NT NT ND ND NT NT 31.1 263 Other HPV ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND *Probes tested only with some A9 plasmids (i.e.. those A9 plasmids. which are indicated in this table) ND: not detected NT: not tested

TABLE 62 A9 System E2 specificity Multiplex A9E2S1 A9E2S2 Simplex Simplex Simplex Simplex A9E2S3a Probes A9E2Z7S1 A9E2Z7S2 A9E2Z7S3a A9E2Z7S4a A9E2S4a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 21.35 806 ND ND ND ND 22.85 113 20.55 333 31 A9 23.8 485 ND ND ND ND 23.5 295 25.3 238 33 A9 32.1 73 27.7 1415  ND ND 27.5 45 31.45 256 35 A9 ND ND ND ND 27.8 840 ND ND 30.1 160 52 A9 25.2 80 22.4 186 ND ND 21.45 278 21.7 115 58 A9 24.45 130 22.1 435 ND ND 23.55 94 24.1 113 67 A9 30.2 173 28.7 447 ND ND 29.35 123 31.9 125 Other HPV ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 63 A9 System E3 specificity Multiplex A9E2S1 A9E2S2 Simplex Simplex Simplex Simplex A9E2S3a Probes A9E2Z7S1 A9E2Z7S2 A9E2Z7S3a 9E2Z7S4a A9E2S4a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 20.5 2000 ND ND ND ND 21.85 520 21 546 31 A9 22.35 1200 ND ND ND ND 22.65 660 25.2 336 33 A9 27.05 250 20.7  1600  ND ND 24.8 135 22.2 496 35 A9 ND ND ND ND 26.95 750 ND ND 31.5 79 52 A9 25.35 300 21.7  370 ND ND 21.65 220 21.7 169 58 A9 32.6 100 22.05 200 ND ND 23.6 180 22.7 189 67 A9 30.05 150 28.95 420 ND ND 29.95 120 NT NT Other HPV ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 64 A9 System E4 specificity Multiplex A9E2S1 A9E2S2 Simplex Simplex Simplex Simplex A9E2S3a Probes A9E2Z7S1 A9E2Z7S2 A9E2Z7S3a A9E2Z7S4a A9E2S4a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 21.05 600.24 ND ND ND ND 23.25 139.94 23.55 473.54 31 A9 22.0 461.14 ND ND ND ND 22.5 447.6 23.65 524.07 33 A9 25.95 68.73 21.65 3190.34 ND ND 24.95 108.385 23.2 800.33 35 A9 ND ND ND ND 21.6 1355.5 ND ND 23.4 348.45 52 A9 26.9 26.58 22.85 314.81 ND ND 21.5 320.785 22.4 207.195 58 A9 26.25 104.23 24.1 899.37 ND ND 24.8 158.91 24.9 357.445 67 A9 24.6 134.345 22.9 1275.03 ND ND 23.85 188.72 NT NT Other HPV ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 65 A9 System F specificity Multiplex A9E2S1 A9E2S2 Simplex Simplex Simplex Simplex A9E2S3a Probes A9E2Z7S1 A9E2Z7S2 A9E2Z7S3a A9E2Z7S4a A9E2S4a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 21.75 765 ND ND ND ND 23.95 77 21.1 335 31 A9 22.4 510 ND ND ND ND 22.05 287 22.7 235 33 A9 27.0 117 21.1 1298.5  ND ND 24.4 61.5 21.1 443 35 A9 ND ND ND ND 21.0 1542.5 ND ND 22.8 154 52 A9 30.95 78.5 25.3 180   ND ND 22.45 399 22.3 199 58 A9 26.05 187.5 23.1 538.5 ND ND 23.05 178 22.2 280 67 A9 25.15 190.5 23.0 569.5 ND ND 23.1 185.5 NT NT Other HPV ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 66 A9 System G Z7 specificity Multiplex A9E2S1 A9E2S2a Simplex Simplex Simplex Simplex A9E2S3a Probes A9E2Z7S1 A9E2Z7S2a A9E2Z7S3a A9E2Z7S4a A9E2S4a N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 20.3 600 ND ND ND ND 24.6 56 21 658 31 A9 20.6 303.5 ND ND ND ND 22.7 167 23.1 501 33 A9 22.9 80 ND ND ND ND 22.1 280 20.4 920 35 A9 ND ND ND ND 22.2 1330 ND ND 23.9 254 52 A9 24.1 53 23 371.5 ND ND 23 284 22.9 519 58 A9 23.1 150 21.6 739 ND ND 23.8 124 21.9 779 67 A9 21.9 191.5 21.7 692 ND ND 23.6 156.5 NT NT Other HPV ND ND ND ND ND ND ND ND NT NT DNA sample ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 67 A9 system G Z8 specificity Simplex Simplex Simplex Simplex Simplex Simplex Probes A9E2Z8S2f A9E2Z8S61f A9E2Z8S127f A9E2Z8S156f A9E2Z8S210f A9E2Z8S250f N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 21.5 261 ND ND ND ND ND ND ND ND ND ND 31 A9 ND ND 21.9 291 ND ND ND ND ND ND ND ND 33 A9 ND ND ND ND 20.5 677 ND ND ND ND ND ND 35 A9 ND ND ND ND ND ND 22.6 333.5 ND ND ND ND 52 A9 ND ND ND ND ND ND ND ND 23.0 115 ND ND 58 A9 ND ND ND ND ND ND ND ND ND ND 20.0 1348 67 A9 ND ND ND ND ND ND ND ND ND ND 22.1 351.5 Other HPV ND ND ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND Multiplex Multiplex A9E2Z8S2f A9E2Z8S2f** A9E2Z8S61f A9E2Z8S61f A9E2Z8S127f A9E2Z8S127f A9E2Z8S156f A9E2Z8S156f A9E2Z8S210f A9E2Z8S210f** Probes A9E2Z8S250f* A9E2Z8S250f* N^(o)HPV Group CT RFU CT RFU 16 A9 22.4 27 22.4 22 31 A9 23.6 73.5 24 42 33 A9 21.8 83.5 20.9 110 35 A9 22.7 42 23.6 45 52 A9 25.8 25 24 30 58 A9 19.3 169 19.6 201 67 A9 21.6 57 NT NT DNA sample ND ND ND ND H₂O sample ND ND ND ND ND: not detected NT: not tested *probe at 0.1 μM in these tests **probes at 0.3 μM in this test

TABLE 68 A9 System H specificity Simplex Simplex Simplex Simplex Simplex Simplex Simplex Probes A9E2Z8S2f A9E2Z8S61f A9E2Z8S127f A9E2Z8S156f A9E2Z8S210f A9E2Z8S231f A9E2Z8S250f N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU CT RFU 16 A9 21.7 665 ND ND ND ND ND ND ND ND ND ND ND ND 31 A9 ND ND 22.1 307 ND ND ND ND ND ND ND ND ND ND 33 A9 ND ND ND ND 21.4 889 ND ND ND ND ND ND ND ND 35 A9 ND ND ND ND ND ND 22.2 155 ND ND ND ND ND ND 52 A9 ND ND ND ND ND ND ND ND 23.9 270 ND ND ND ND 58 A9 ND ND ND ND ND ND ND ND ND ND 21.3 345 19.8 2690 67 A9 ND ND ND ND ND ND ND ND ND ND 27.0 82.5 27.1  276 Other HPV ND ND ND ND ND ND ND ND ND ND ND ND ND ND DNA sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND ND ND ND ND ND Multiplex Multiplex Multiplex Multiplex A9E2Z8S2f A9E2Z8S2f A9E2Z8S2f A9E2Z8S2f A9E2Z8S61f A9E2Z8S61f A9E2Z8S61f A9E2Z8S61f A9E2Z8S127f A9E2Z8S127f A9E2Z8S127f A9E2Z8S127f A9E2Z8S156f A9E2Z8S156f A9E2Z8S156f A9E2Z8S156f A9E2Z8S210f A9E2Z8S210f A9E2Z8S210f A9E2Z8S210f Probes A9E2Z8S250f A9E2Z8S231f A9E2Z8S250f A9E2Z8S231f N^(o)HPV Group CT RFU CT RFU CT RFU CT RFU 16 A9 21.9 143 21.9 167 21.7 106 22.9 98 31 A9 21.5 81 21.9 101 21.6 50 22.5 62 33 A9 22.7 114 22.5 155 22.2 93 22.2 158 35 A9 22.5 63 22.4 70 22.4 46 22.9 48 52 A9 23.7 44 25.4 50 24.6 15 25.0 39 58 A9 19.7 403 19.9 280 19.1 398 19.7 255 67 A9 29.0 29 29.1 26 27.6 16 27.0 38 DNA sample ND ND ND ND ND ND ND ND H₂O sample ND ND ND ND ND ND ND ND ND: not detected NT: not tested

TABLE 69 A5 Systems A, B, C, D, E/sensitivity System A System B System C A5E6S1/HPV51 A5E6S1b/HPV51 A5E6S2/HPV51 A5E6S3/HPV51 Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10³ cop/PCR 27.95 2700 25.65 1100 27.3 180 24.3 430 10² cop/PCR 31.3 2500 29.75 1000 31.0 180 26.85 380  10 cop/PCR 34.85 2200 34.3 700 35.7 160 30.0 280   1 cop/PCR 36.95 1700 36.65 450 38.85 150 33.1 180 H2O sample ND ND ND ND ND ND ND ND ADN Sample ND ND ND ND ND ND ND ND r2/slope/PCR efficiency 0.997/−2.988/116.1% 0.997/−3.647/88% 0.990/−3.924/79.8% 0.997/−2.955/118% System D System E Copy number HPV A5E6S4/HPV51 A5E6S4/HPV51 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs 10³ cop/PCR  31.45 750 24.55 500 10² cop/PCR 35.1 700 27.45 450  10 cop/PCR 39.7 500 31.15 450   1 cop/PCR 43.2 250 33.75 500 H2O sample ND ND ND ND ADN Sample ND ND ND ND r2/slope/PCR efficiency 0.994/−3.990/78.1% 0.997/−3.128/108.8% ND: No Detection NT: Not tested

TABLE 70 A6 Systems A, B, C, D, E/sensitivity System A System B System C Copy number HPV A6E6S1/HPV56 A6E6S1/HPV56 A6E6S2/HPV56 A6E6S2b/HPV56 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10³ cop/PCR 27.25 400 27.1 600 33.955 1700 29.55 650 10² cop/PCR 27.8 450 27.9 700 35.78 1500 33.1 550  10 cop/PCR 30.8 450 30.75 700 38.89 1200 38.25 300   1 cop/PCR 34.25 350 34.15 450 43.09 600 ND ND H2O sample ND ND ND ND ND ND ND ND ADN Sample ND ND ND ND ND ND ND ND r2/slope/PCR 0.974/−3.228/104.1% 0.997/−3.16/107% 0.989/−3.270/102.2% 0.998/−3.699/86.4% efficiency System D System E Copy number HPV A6E6S1/HPV56 A6E6S3/HPV56 A6E6S3b/HPV56 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10³ cop/PCR 28.95 750 26.1 600 27.5 750 10² cop/PCR 30.75 750 27.45 650 30.35 750  10 cop/PCR 33.65 800 30.45 550 33.9 600   1 cop/PCR 35.4 700 32.15 550 ND ND H2O sample ND ND ND ND ND ND ADN Sample ND ND ND ND ND ND r2/slope/PCR 0.987/−2.461/154.8% 0.986/−2.126/195.4% 0.990/−3.183/106.1% efficiency ND: No detection NT: Not tested

TABLE 71 A7 System A, sensitivity copy number HPV plasmid/ A7E1ZAS61f HPV 18 A7E1S63f HPV 59 A7E1S64f HPV 39 A7E1S40f HPV 45 PCR Moy Ct Moy RFU Moy Ct Moy RFUs Moy Ct Moy RFUs Ecart-type Moy RFUs 10⁶ cop/PCR 22.7 165 21.7 125 22.1 240 24.6 305 10⁵ cop/PCR 25.95 170 24.6 95 25.0 310 27.45 320 10⁴ cop/PCR 29.15 180 27.1 125 28.3 320 30.6 310 10³ cop/PCR 32.6 180 31.0 105 31.1 350 33.85 272.5 10² cop/PCR 35.2 170 33.95 70 34.15 290 36.9 282.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.997/−3.16/107% 0.993/−3.1/110% 0.996/−3.19/106% 0.995/−3.27/102% copy number HPV plasmid/ A7E1ZBS74f HPV 68 A7E1ZBS74f HPV 39 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 24.2 597.585 22.5 1095.195 10⁵ cop/PCR 26.85 611.52 25.25 1182.205 10⁴ cop/PCR 31.15 557.525 28.05 1062.505 10³ cop/PCR 35.35 496.425 32.45 1005.26 10² cop/PCR 39.5 473.395 40.6 804 H₂O sample ND ND ND ND ADN sample ND ND ND ND r2/slope/efficiency PCR 0.995/−3.919/80% 0.972/−3.271/102.2% ND: no Detection NT: no test

TABLE 72 A7 System B. sensitivity A7E1ZBS26f A7E1ZBS26f A7E1ZBS74f A7E1ZBS74f copy number HPV plasmid/ HPV 18 HPV 45 HPV 68 HPV 39 PCR Moy Ct Moy RFU Moy Ct Moy RFUs Moy Ct Moy RFUs Ecart-type Moy RFUs 10⁶ cop/PCR 21.35 222.5 22.1 115 21.2 705 24.85 892.5 10⁵ cop/PCR 23.05 252.5 24.75 130 24.7 690 27.0 852.5 10⁴ cop/PCR 26.5 225 28.05 115 28.15 645 31.2 632.5 10³ cop/PCR 28.6 180 29.7 112.5 30.85 540 32.65 445 10² cop/PCR 31.35 155 30.85 112.5 33.25 390 31.85 660.5 H₂O sample ND ND ND ND 42.5 64 42.5 64 ADN sample ND ND ND ND ND 23 ND 23 r2/slope/efficiency PCR 0.987/−2.55/146% 0.970/−2.24/179% 0.995/−3.02/114% 0.887/−1.96/223% A7E1ZBS80f A7E1ZBS79f A7E1ZBS27f A7E1ZBS27f copy number HPV plasmid/ HPV 59 HPV 59 HPV 45 HPV 18 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.65 952.5 18.85 387.5 20.3 675 20.9 112.5 10⁵ cop/PCR 21.85 1025 21.5 427.5 23.25 595 24.35 117.5 10⁴ cop/PCR 23.75 997.5 24.1 405 26.3 557.5 28 122.5 10³ cop/PCR 27.1 952.5 26.25 412.5 27.8 502.5 31.7 137.5 10² cop/PCR 31.7 907.5 29.0 377.5 33.05 440 31.05 157.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.981/−2.94/119% 0.976/−2.51/150% 0.973/−3.01/115% 0.934/−2.718/133.3% ND: no Detection NT: no test

TABLE 73 A7 System C. sensitivity A7E1ZCS11f/ A7E1ZCS45f/ A7E1ZCS63f/ A7E1ZCS90f/ copy number HPV plasmid/ HPV 45 HPV 39 HPV 59 HPV 68 PCR Moy Ct Moy RFU Moy Ct Moy RFUs Moy Ct Moy RFUs Ecart-type Moy RFUs 10⁶ cop/PCR 21.95 349.45 20.35 649.815 23.1 256.71 24.05 234.305 10⁵ cop/PCR 24.7 344.81 23.4 623.445 26.4 224.625 27.0 200 10⁴ cop/PCR 28.35 274.81 26.95 502.52 28.9 178.505 30.5 140.205 10³ cop/PCR 31.6 154.565 30.35 364.095 33.0 107.145 33.4 92.505 10² cop/PCR 35.1 48.72 33.45 173.17 35.3 49.965 37.15 46.65 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.997/−3.321/100% 0.998/−3.322/100% 0.993/−3.111/109.9% 0.998/−3.255/102.9% A7E1ZCS11f/ A7E1ZCS40f/ A7E1ZCS40f/ A7E1ZCS40f/ copy number HPV plasmid/ HPV 18 HPV 18 HPV 45 HPV 59 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.05 247.645 23.6 65.31 23.65 161.135 22.25 9.985 10⁵ cop/PCR 24.45 230.285 26.25 79.255 27.5 138.725 22.65 27.19 10⁴ cop/PCR 27.1 197.085 29.95 56.015 29.85 107.025 28.7 11.595 10³ cop/PCR 31.35 94.76 34.2 29.31 37.9 14 N/A ND 10² cop/PCR 35.0 12.61 N/A ND N/A ND N/A ND H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.993/−3.275/102% 0.986/−3.55/91.3% 0.988/−3.079/111.3% 0.922/−4.269/71.5% ND: no Detection NT: no test

TABLE 74 A7 System D. sensitivity A7E1ZDS36f A7E1ZDS37f A7E1ZDS38f A7E1ZDS38f copy number HPV plasmid/ HPV 45 HPV 18 HPV 59 HPV 39 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 26.0 705 21.9 305 21.05 525 24.2 190 10⁵ cop/PCR 29.5 645 25.55 302.5 25.35 487.5 27.8 192.5 10⁴ cop/PCR 33.25 537.5 27.1 292.5 29.2 402.5 32.25 155 10³ cop/PCR 36.95 440 30.95 265 32.5 335 35.95 147.5 10² cop/PCR 40.0 332.5 32.45 247.5 33.7 342.5 39.2 140 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.998/−3.622/88.8% 0.978/−2.652/138.3% 0.981/−3.253/103% 0.995/−3.805/83.2% copy number HPV plasmid/ A7E1ZDS2f HPV 68 A7E1ZDS2f HPV 39 A7E1ZDS3f HPV 45 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 23.1 942 21.15 113.5 21.85 2075 10⁵ cop/PCR 26.8 898.5 25.55 97.5 24.9 1875 10⁴ cop/PCR 30.5 842.5 28.8 87.5 27.75 1617.5 10³ cop/PCR 33.15 677.5 32.25 79 31.05 1250 10² cop/PCR 36.65 635 31.75 80 34.2 1007.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND 36.1 ND ND ND r2/slope/efficiency PCR 0.995/−3.334/99.5% 0.941/−2.797/127.8% 0.999/−3.086/110.9% ND: no Detection NT: no test

TABLE 75 A9 System C, sensitivity copy number HPV plasmid/ A9E1S10a/HPV 16 A9E1S10a/HPV 31 A9E1S10a/HPV 33 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.4 457.5 22.15 477 22.5 410 10⁵ cop/PCR 27.2 402.5 26.45 360 28.2 344 10⁴ cop/PCR 30.85 341 29.9 342 31.0 306.5 10³ cop/PCR 34.3 322.5 33.2 316.5 34.35 272 10² cop/PCR 37.35 320 36.7 259.5 37.1 227.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.996/−3.705/86.2% 0.998/−3.586/90.0% 0.987/−3.536/91.8% copy number HPV plasmid/ A9E1S10a/HPV 35 A9E1S10a/HPV 52 A9E1S10a/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 24.4 233.5 21.85 650 23.65 620 10⁵ cop/PCR 29.0 202 26.4 507 28.3 558.5 10⁴ cop/PCR 32.65 192 29.9 474.5 32.3 484 10³ cop/PCR 36.25 167 33.55 429.5 35.95 422.5 10² cop/PCR 39.45 135.5 36.7 350.5 39.35 271.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.997/−3.735/85.2% 0.997/−3.680/87.0% 0.997/−3.915/80.1% copy number HPV plasmid/ A9E1S10a/HPV 67 A9E1S12a/HPV 31 A9E1S12a/HPV 35 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.0 351 26.45 61 22.45 504 10⁵ cop/PCR 25.95 339 31.3 53.5 27.6 469.5 10⁴ cop/PCR 29.75 304 32.2 67 31.3 452 10³ cop/PCR 33.05 261.5 36.25 56 34.25 419.5 10² cop/PCR 36.45 222.5 39.45 51 37.7 356.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.999/−3.594/89.8% 0.971/−3.099/110.2% 0.994/−3.719/85.7% ND: not detected NT: not tested

TABLE 76 A9 System E2, sensitivity A9E2Z7S1/HPV 16 A9E2Z7S1/HPV 31 A9E2Z7S1/HPV 33 A9E2Z7S1/HPV 52 copy number HPV plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.8 795 23.05 485 31.35 88.5 24.25 86 10⁵ cop/PCR 24.1 765 26.5 425 34.4 83.5 27.05 82.5 10⁴ cop/PCR 27.3 705 29.8 385 38.1 65 30.8 78.5 10³ cop/PCR 31.5 610 33.0 342.5 42.8 35 33.85 77.5 10² cop/PCR 34.95 287.5 37.25 177.5 38.9 41.5 36.2 82.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.996/−3.767/84.3% 0.998/−3.492/93.4% 0.869/−2.762/130.2% 0.996/−3.069/111.7% A9E2Z7S1/HPV 58 A9E2Z7S1/HPV 67 A9E1Z7S2/HPV 33 A9E1Z7S2/HPV 58 copy number HPV plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 23.4 145 29.35 120.5 26.4 1257.5 20.95 485 10⁵ cop/PCR 26.4 140 32.85 105 30.0 1120 24.35 395 10⁴ cop/PCR 30.45 125 36.9 77.5 33.6 877.5 28.15 340 10³ cop/PCR 34.35 95 42.4 37.5 37.05 520 31.85 310 10² cop/PCR 37.05 91 ND ND 40.0 107.5 34.7 257.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.99/−3.525/90.2% 0.991/−4.333/70.1% 0.993/−3.431/95.7% 0.999/−3.508/92.8% A9E1Z7S2/HPV 52 A9E1Z7S2/HPV 67 A9E1Z7S3a/HPV 35 copy number HPV plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 21.1 182.5 26.6 473 27.25 825 10⁵ cop/PCR 24.65 197.5 30.4 430 30.85 807.5 10⁴ cop/PCR 28.15 192.5 33.2 390 34.5 505 10³ cop/PCR 31.85 182.5 35.7 200 37.9 82.5 10² cop/PCR 34.95 162.5 40.3 115 40.4 47.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.999/−3.480/92.8% 0.989/−3.279/101.8% 0.990/−3.396/97% A9E2Z7S4a/HPV 31 A9E2Z7S4a/HPV 52 A9E2Z7S4a/HPV 16 copy number HPV plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 23.2 460 21.45 485 21.85 182.5 10⁵ cop/PCR 26.5 452.5 24.5 425 25.6 177.5 10⁴ cop/PCR 29.85 435 28.35 385 29.8 147.5 10³ cop/PCR 34.05 322.5 31.65 340 33.75 135 10² cop/PCR 38.0 165 35.55 280 36.2 145 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.998/−3.720/85.7% 0.996/−3.517/92.5% 0.996/−3.687/86.7% A9E2Z7S4a/HPV 33 A9E2Z7S4a/HPV 58 A9E2Z7S4a/HPV 67 copy number HPV plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 32.0 57.5 23.6 115 28.45 177.5 10⁵ cop/PCR 35.0 57.5 27.2 122.5 32.0 140 10⁴ cop/PCR 43.6 31 31.5 87.5 36.3 107.5 10³ cop/PCR ND ND 34.1 90 42.8 42.5 10² cop/PCR ND ND 40.4 50 46.7 20 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.938/−5.797/48..8% 0.980/−4.047/76.6% 0.981/−4.736/62.6% ND: not detected NT: not tested

TABLE 77 A9 System E3, sensitivity copy number HPV plasmid/ A9E2Z7S1/HPV 16 A9E2Z7S1/HPV 31 A9E2Z7S1/HPV 33 A9E2Z7S1/HPV 52 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 18.0 725 19.7 457 22.8 69 20.3 59 10⁵ cop/PCR 20.3 754 23.7 428 26.9 58 22.7 77 10⁴ cop/PCR 23.3 692 25.5 390 30.2 55 24.7 97 10³ cop/PCR 26.2 611 29.4 322 34.1 48 28.4 73 10² cop/PCR 30.0 476 32.6 208 37.2 29 32.2 65 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.994/−2.994/115.8% 0.994/−3.148/107.8% 0.988/−3.647/88% 0.987/−2.952/118.2% copy number HPV plasmid/ A9E2Z7S1/HPV 58 A9E2Z7S1/HPV 67 A9E1Z7S2/HPV 33 A9E1Z7S2/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 20.8 117 27.5 111  16.7 1741 20.8 636 10⁵ cop/PCR 22.5 113 29.4 110  19.2 1767 22.5 537 10⁴ cop/PCR 24.9 123 33.1 99 22.7 1574 24.9 693 10³ cop/PCR 28.4 117 36.9 70 26.9 1473 28.4 465 10² cop/PCR 31.3 104 41.3 30 29.6 1172 31.3 357 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.987/−2.296/134.9% 0.990/−3.509/92.7% 0.995/−3.318/100.1% 0.772/−2.474/153.6% copy number HPV plasmid/ A9E1Z7S2/HPV 52 A9E1Z7S2/HPV67 A9E1Z7S3a/HPV 35 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 18.6 393 25.3 433 25.3 869 10⁵ cop/PCR 21.1 303 28.8 375 27.6 611 10⁴ cop/PCR 25.1 274 31.8 299 31.6 509 10³ cop/PCR 28.0 260 35.4 214 34.7 294 10² cop/PCR 32.4 152 ND ND ND ND H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.994/−3.523/92.3% 0.997/−3.323/99.9% 0.993/−3.328/104.1% copy number HPV plasmid/ A9E2Z7S4a/HPV 31 A9E2Z7S4a/HPV 52 A9E2Z7S4a/HPV 16 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.2 494 18.1 427 18.9  79 10⁵ cop/PCR 22.8 451 20.2 473 21.0 199 10⁴ cop/PCR 26.0 360 23.7 460 23.7 170 10³ cop/PCR 29.5 283 27.5 419 27.2 166 10² cop/PCR 33.4  82 31.0 273 31.3  37 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.998/−3.510/92.7% 0.995/−3.312/100.4% 0.989/−3.006/115.1% copy number HPV plasmid/ A9E2Z7S4a/HPV 33 A9E2Z7S4a/HPV 58 A9E2Z7S4a/HPV 67 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 21.0 66 19.7 105 27.2 494 10⁵ cop/PCR 24.2 62 22.8 108 30.5 451 10⁴ cop/PCR 27.5 56 25.8 108 36.1 360 10³ cop/PCR 30.8 53 30.3  78 45.4 283 10² cop/PCR ND 22 35.6  57 ND ND H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.994/−3.257/102.8% 0.976/−3.920/79.9% 0.959/−5.655/50.3% ND: not detected NT: not tested

TABLE 78 A9 System E4, sensitivity copy number HPV A9E2Z7S1/HPV 16 A9E2Z7S1/HPV 31 A9E2Z7S1/HPV 52 A9E2Z7S1/HPV 33 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.8 915 21.45 795 24.25 65 24.35 105 10⁵ cop/PCR 23.25 940 24.3 717.5 31.1 47.5 28.65 90 10⁴ cop/PCR 26.75 840 28.25 540 37.8 27 37.8 83 10³ cop/PCR 30.85 615 32.5 412.5 35.15 40 36.15 75 10² cop/PCR 34.95 507.5 35.0 272.5 37.3 37.5 38.95 47.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.993/−3.789/83.7% 0.996/−3.509/92.8% 0.889/−3.017/114.5% 0.996/−3.664/87.5% copy number HPV A9E2Z7S1/HPV 58 A9E2Z7S1/HPV 67 A9E1Z7S2/HPV 33 A9E1Z7S2/HPV 58 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 23.8 157.5 22.9 207.5 22.0 2871.625 22.75 903.92 10⁵ cop/PCR 27.6 167.5 26.45 190 25.7 2916.84 25.95 822.335 10⁴ cop/PCR 37.8 128 37.8 160 29.95 2525.075 29.55 731.815 10³ cop/PCR 36.0 90 34.25 122.5 33.55 1574.41 33.95 614.88 10² cop/PCR 39.8 45 39.8 52.5 37.45 1675.46 37.35 155.27 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.999/−4.075/75.9% 0.996/−4.075/75.9% 0.998/−3.866/81.4% 0.998/−3.725/85.5% copy number HPV plasmid/ A9E1Z7S2/HPV 52 A9E1Z7S2/HPV67 A9E1Z7S3a/HPV 35 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 20.4 372.5 21.3 1225 22.6 1085.81 10⁵ cop/PCR 23.6 360 24.35 1157.5 26.1 1037.5 10⁴ cop/PCR 27.2 345 27.9 1055 29.6 932.32 10³ cop/PCR 30.85 347.5 31.75 935 33.75 730.08 10² cop/PCR 34.65 310 35.85 757.5 38.55 501.76 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.997/−3.586/90.1% 0.998/−3.641/88.2% 0.997/−3.960/78.9% copy number HPV plasmid/ A9E2Z7S4a/HPV 31 A9E2Z7S4a/HPV 52 A9E2Z7S4a/HPV 16 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 21.8 800 20.45 640 22.35 267.5 10⁵ cop/PCR 25.2 747.5 24.0 600 25.0 260 10⁴ cop/PCR 28.4 665 27.5 562.5 29.55 240 10³ cop/PCR 33.3 505 30.95 532.5 32.75 210 10² cop/PCR 37.2 335 34.4 422.5 33.55 207.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.996/−3.872/81.2% 1/−3.476/94% 0.976/−3.010/114.9% copy number HPV plasmid/ A9E2Z7S4a/HPV 33 A9E2Z7S4a/HPV 58 A9E2Z7S4a/HPV 67 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 24.45 212.5 24.2 340 23.25 415 10⁵ cop/PCR 27.3 230 27.45 305 25.55 407.5 10⁴ cop/PCR 31.1 205 31.2 250 30.5 312.5 10³ cop/PCR 35.1 162.5 34.35 187.5 33.75 277.5 10² cop/PCR 36.8 127.5 38.9 117.5 38.2 145 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.991/−3.264/102.5% 0.998/−3.632/88.5% 0.989/−3.810/83% ND: not detected NT: not tested

TABLE 79 A9 System F, sensitivity copy number HPV plasmid/ A9E2Z7S1/HPV 16 A9E2Z7S1/HPV 31 A9E2Z7S1/HPV 33 A9E2Z7S1/HPV 52 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.45 1815 19.85 1227.5 23.85 63 25.25 40 10⁵ cop/PCR 22.25 1727.5 22.95 1215 27.1 63 28.55 41.5 10⁴ cop/PCR 26.1 1665 26.75 1150 30.55 62.5 31.6 37.5 10³ cop/PCR 26.65 1535 29.6 1055 33.9 62 35.4 41 10² cop/PCR 33.15 1312.5 35.2 753.5 37.8 47.5 38.25 34 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.969/−3.202/105.2% 0.990/−3.739/85.1% 0.999/−3.487/93.5% 0.998/−3.651/87.9% copy number HPV plasmid/ A9E2Z7S1/HPV 58 A9E2Z7S1/HPV 67 A9E1Z7S2/HPV 33 A9E1Z7S2/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.8 132.5 22.85 138 20.2 3013.235 21.75 1330.945 10⁵ cop/PCR 26.1 125 25.95 127.5 23.4 3085.8 24.85 1292.96 10⁴ cop/PCR 29.55 120 29.6 120 26.7 2967.135 28.35 1266.585 10³ cop/PCR 33.45 107 33.65 96 30.45 2499.875 32.25 973.095 10² cop/PCR 37.4 100 35.85 100 33.8 2129.57 35.55 841.57 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.998/−3.651/87.9% 0.993/−3.366/98.20% 0.999/−3.435/95.5% 0.999/−3.502/93% copy number HPV plasmid/ A9E1Z7S3a/HPV 35 A9E2Z7S4a/HPV 31 A9E2Z7S4a/HPV 52 A9E2Z7S4a/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.1 1337.995 21.85 705 21.75 1022.5 22.1 522.5 10⁵ cop/PCR 25.05 1354.145 24.1 730 24.25 992.5 24.55 460 10⁴ cop/PCR 29.4 1254.22 27.9 665 27.65 1002.5 28.9 455 10³ cop/PCR 33.25 1018.5 30.5 560 31.05 957.5 31.5 465 10² cop/PCR 37.0 678.815 35.25 430 34.7 650 35.2 382.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.996/−3.799/83.3% 0.989/−3.332/99.6% 0.996/−3.273/102.1% 0.994/−3.317/100.2% copy number HPV A9E2Z7S4a/HPV 67 A9E2Z7S4a/HPV 16 A9E2Z7S4a/HPV 33 plasmid/PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.15 570 21.95 195 22.45 240 10⁵ cop/PCR 24.2 670 24.65 227.5 25.15 245 10⁴ cop/PCR 28.75 555 29.2 196 29.7 255 10³ cop/PCR 31.2 460 32.6 187.5 32.55 187.5 10² cop/PCR 32.7 447.5 35.7 185 36.45 165 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.964/−2.805/127.3% 0.994/−3.487/93.5% 0.995/−3.538/91.7% ND: not detected NT: not tested

TABLE 80 A9 System G Z7, sensitivity copy number HPV plasmid/ A9E2Z7S1/HPV 16 A9E2Z7S1/HPV 31 A9E2Z7S1/HPV 33 A9E2Z7S1/HPV 52 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 20.25 771 20.85 468 22.85 113 23.2 82 10⁵ cop/PCR 23.55 713.5 24.5 419.5 26.4 119 26.45 75 10⁴ cop/PCR 27.0 654 27.6 375.5 30.8 79.5 29.65 65 10³ cop/PCR 30.75 527 31.15 289 33.6 71 33.35 48.5 10² cop/PCR 34.45 296.5 35.1 186 37.3 44.5 37.05 30.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.999/−3.557/91% 0.998/−3.520/92.3% 0.996/−3.612/89.2% 0.998/−3.452/94.9% copy number HPV plasmid/ A9E2Z7S1/HPV 58 A9E2Z7S1/HPV 67 A9E1Z7S2a/HPV 33 A9E1Z7S2a/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.15 187.5 21.8 207 19.8 1165 20.65 717 10⁵ cop/PCR 25.75 165.5 24.9 199 23.1 1080.5 23.75 682 10⁴ cop/PCR 28.8 147 27.35 182.5 26.3 1015.5 27.35 603.5 10³ cop/PCR 32.45 100 32.05 128.5 30.05 844 30.9 426 10² cop/PCR 35.35 63 35.4 78.5 33.65 605.5 34.8 234 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.998/−3.313/100.4% 0.993/−3.425/95.9% 0.998/−3.469/94.2% 0.998/−3.558/91% copy number HPV plasmid/ A9E1Z7S3a/HPV 35 A9E2Z7S4a/HPV 31 A9E2Z7S4a/HPV 52 A9E2Z7S4a/HPV 58 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.15 883.5 21.7 187.5 21.65 257 22.35 145 10⁵ cop/PCR 25.3 795 25.95 180.5 26.45 268 26.05 136.5 10⁴ cop/PCR 29.0 674.5 29.7 157.5 29.8 220 29.3 116 10³ cop/PCR 32.2 546 33.4 128.5 33.6 155 33.65 80 10² cop/PCR 35.2 300 36.65 71 37.9 69 37.3 40 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.999/−3.656/87.7% 0.999/−3.727/85.5% 0.997/−3.967/78.7% 0.998/−3.751/84.7% copy number HPV plasmid/ A9E2Z7S4a/HPV 67 A9E2Z7S4a/HPV 16 A9E2Z7S4a/HPV 33 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.4 159 22.4 67 22.65 69.5 10⁵ cop/PCR 26.5 155.5 27.7 63 27.0 60 10⁴ cop/PCR 30.1 134 31.0 60 30.25 58.5 10³ cop/PCR 34.35 90.5 34.6 46 33.4 51.5 10² cop/PCR 38.55 33 38.4 23.5 37.8 32.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.996/−4.035/76.9% 0.996/−3.894/80.6% 0.996/−3.670/87.3% ND: not detected NT: not tested

TABLE 81 A9 System G Z8, sensitivity copy number HPV plasmid/ A9E2Z8S2f/HPV16 A9E2Z8S61f/HPV 31 A9E2Z8S127f/HPV 33 A9E2Z8S156f/HPV35 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 20.9 275 20.8 439.5 20.4 357 21.85 347.5 10⁵ cop/PCR 24.65 274.5 25.25 382 24.95 322 25.75 334.5 10⁴ cop/PCR 27.85 270 29.1 328 28.75 300.5 29.25 331.5 10³ cop/PCR 31.55 217 32.3 242 31.6 261.5 32.8 243 10² cop/PCR 35.3 107.5 36.3 86 37.0 98 36.45 121 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.995/−3.587/90% 0.995/−3.799/83.3% 0.995/−3.990/78.1% 0.997/−3.639/88.3% copy number HPV plasmid/ A9E2Z8S210f/HPV52 A9E2AZ8S250f/HPV58 A9E2AZ8S250f/HPV67 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 22.05 32 19.3 728 21.2 173 10⁵ cop/PCR 25.65 57 22.6 663 26.2 152 10⁴ cop/PCR 27.45 54.5 26.0 728 29.6 157 10³ cop/PCR 32.7  31 29.7 627 32.6 149 10² cop/PCR 37.75 14 32.9 457 36.6  98 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.976/−3.880/81% 0.999/−3.425/95.9% 0.994/−3.701/86.3% ND: not detected NT: not tested

TABLE 82 A9 System H, sensitivity A9E2Z8S61f/ A9E2Z8S127f/ A9E2Z8S156f/ copy number HPV plasmid/ A9E2Z8S2f/HPV16 HPV 31 HPV 33 HPV35 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 20.55 567.5 20.55 570 20.25 550 21.2 435 10⁵ cop/PCR 23.7 530 23.25 530 23.7 490 24.55 437.5 10⁴ cop/PCR 27.2 465 27.05 507.5 27.4 482.5 28.1 375 10³ cop/PCR 31.85 395 29.8 400 31.5 450 32.95 250 10² cop/PCR 34.3 220 34.05 247.5 35.35 212.5 37.05 172.5 H₂O sample ND ND ND ND ND ND ND ND ADN sample ND ND ND ND ND ND ND ND r2/slope/efficiency PCR 0.99/−3.570/90.6% 0.995/−3.352/98.8% 0.988/−3.805/83.2% 0.995/−4.011/77.5% A9E2Z8S210f/ A9E2AZ8S250f/ A9E2AZ8S250f/ copy number HPV plasmid/ HPV52 HPV58 HPV67 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 21.65 240 20.15 2300 27.5 150 10⁵ cop/PCR 25.95 225 23.0 2405 32.3 100 10⁴ cop/PCR 30.2 170 26.6 2350 35.2 62.5 10³ cop/PCR 34.3 100 30.55 1800 37.55 82.5 10² cop/PCR 36.65 75 33.45 1387.5 40.2 52.5 H₂O sample ND ND ND ND ND ND ADN sample ND ND ND ND ND ND r2/slope/efficiency PCR 0.988/−3.837/82.2% 0.993/−3.425/95.9% 0.976/−3.131/108.6% A9E2AZ8S231f/ A9E2AZ8S231f/ copy number HPV plasmid/ HPV58 HPV67 PCR Moy Ct Moy RFUs Moy Ct Moy RFUs 10⁶ cop/PCR 19.75 295 25.45 47.5 10⁵ cop/PCR 22.95 287.5 29.4 47.5 10⁴ cop/PCR 26.4 272.5 33.1 38.5 10³ cop/PCR 30.35 210 35.8 28.5 10² cop/PCR 33.65 147.5 36.15 28.5 H₂O sample ND ND ND ND ADN sample ND ND ND ND r2/slope/efficiency PCR 0.996/−3.525/92.2% 0.945/−2.778/129.1% ND: not detected NT: not tested

TABLE 83 Megaplex A5 E A6 A A7 A A9 H Kit Kit Quantitect probe PCR MgCl₂ 5 mM Plasmid concentration 10⁶ cop/PCR Thermoprofile 52° C. Taq 7U/well Cycling 42x forward primer reverse primer probes Name μM Name μM Name μM A5 System A5E6f5 0.4 A5E6r5 0.4 A5E6s4 0.2 E A6 System A6E6f1 0.4 A6E6r1 0.4 A6E6s1 0.2 A A7 System A7E1-6f1a 0.3 A7E1-6r1b 0.3 A7E1ZCS40f 0.2 A A7E1-6f2a 0.3 A7E1-6r2b 0.3 A7E1ZAS61f 0.2 A7E1-6f3a 0.3 A7E1-6r3b 0.3 A7E1ZAS63f 0.2 A7E1ZBS74f 0.2 A9 System A9E2f6 0.4 A9E2r10 0.6 A9E2Z8S2f 0.2 H A9E2f8 0.4 A9E2r12B 0.4 A9E2Z8S61f 0.2 A9E2f9 0.6 A9E2r15 0.4 A9E2Z8S127f 0.2 A9E2r16 0.4 A9E2Z8S156f 0.2 A9E2Z8S210f 0.2 A9E2Z8S250f 0.1

TABLE 84 specificity of megaplex EAAH Megaplex N^(o)HPV Group CT RFU 51 A5 21.9 226 26 ND ND 69 NT NT 82 ND ND 56 A6 24.4 220 30 ND ND 53 ND ND 66 ND ND 18 A7 23.3 148 39 22.1 182 45 23.1 215 59 24.8 194 68 24.1 169 85 ND ND 70 NT NT 16 A9 24.0 136 16 24.0 136 31 22.5 121 33 22.6 173 35 23.6 94 52 24.1 102 58 21.7 268 67 32.7 25 DNA sample ND ND H₂O sample ND ND ND: no detection NT: not tested

TABLE 85 Megaplex A5 E A6 B A7 A A9 C Kit Kit Quantitect probe PCR MgCl₂ 5 mM Plasmid concentration 10⁶ cop/PCR Thermoprofile 52° C. Taq 7U/well Cycling 42x Name μM Name μM Name μM A5 System E A5E6f5 0.4 A5E6r5 0.4 A5E6s4 0.2 A6 System B A6E6f1 0.6 A6E6r1 0.6 A6E6s1 0.4 A7 System A7E1-6f1a 0.5 A7E1-6r1b 0.3 A7E1ZCS40f 0.2 A A7E1-6f2a 0.3 A7E1-6r2b 0.5 A7E1ZAS61f 0.2 A7E1-6f3a 0.3 A7E1-6r3b 0.3 A7E1ZAS63f 0.2 A7E1ZBS74f 0.2 A9 System C A9E1-f8 0.6 A9E1-r5 0.6 A9E1s10a 0.2 A9E1-f10 0.6 A9E1-r6 0.6 A9E1s12a 0.2 A9E1-f12 0.2 A9E1-f13 0.4

TABLE 86 specificity of megaplex EBAC Megaplex N^(o) HPV Group CT RFU 51 A5 23.3 229 26 ND ND 69 NT NT 82 ND ND 56 A6 24 458 30 ND ND 53 36 170 66 ND ND 18 A7 23.7 110 39 23.8 185 45 23.8 205 59 29 47 68 28.3 107 85 ND ND 70 NT NT 16 A9 24.0 333 16 24.0 333 31 24.1 321 33 23.3 364 35 24.6 347 52 22.7 390 58 22 395 67 22.8 303 DNA sample ND ND H₂O sample ND ND ND: no Detection NT: not tested

TABLE 87 Megaplex A5 E/A6 A/A7 A/A9 H; HPV16 and 18 sensitivity copy number HPV plasmid/ HPV 16 HPV 18 PCR Moy Ct Moy RFU Moy Ct Moy RFUs 10⁶ cop/PCR 25.5 50 25.2 33 10⁵ cop/PCR 28.1 87 27.9 79 10⁴ cop/PCR 31.3 106  31.1 72 10³ cop/PCR 35.0 98 34.3 53 10² cop/PCR 37.9 51 37.9 27 H₂O sample ND ND ND ND ADN sample ND ND ND ND r2/slope/efficiency PCR 0.989/−3.16/107% 0.989/−3.17/107% ND: not detected NT: not tested

TABLE 88 Megaplex A5 E/A6 B/A7 A/A9 C; HPV16 and 18 sensitivity copy number HPV plasmid/ HPV 16 HPV 18 PCR Moy Ct Moy RFU Moy Ct Moy RFUs 10⁶ cop/PCR 24.3 278 24.3  55 10⁵ cop/PCR 26.8 475 28.1 154 10⁴ cop/PCR 29.9 410 31.5 190 10³ cop/PCR 31.2 412 34.3 271 10² cop/PCR 35.8 277 38.0 148 H₂O sample ND ND ND ND ADN sample ND ND ND ND r2/slope/efficiency PCR 0.984/−2.76/130% 0.995/−3.36/98.5% ND: not detected NT: not tested

TABLE 89 list of HPV sequences Organism Type Accession number human  1 a NC_001356 human  2 a NC_001352 human  3 NC_001588 human  4 NC_001457 human  5 NC_001531 human  5 b NC_001444 human  6 NC_000904 human  6 a NC_001668 human  6 b NC_001355 human  7 NC_001595 human  8 NC_001532 human  9 NC_001596 human 10 NC_001576 human 11 NC_001525 human 12 NC_001577 human 13 NC_001349 human 14 D NC_001578 human 15 NC_001579 human 16 AF472509 human 16 NC_001526 human 17 NC_001580 human 18 NC_001357 human 19 NC_001581 human 20 NC_001679 human 21 NC_001680 human 22 NC_001681 human 23 NC_001682 human 24 NC_001683 human 25 NC_001582 human 26 NC_001583 human 27 NC_001584 human 28 NC_001684 human 29 NC_001685 human 30 NC_001585 human 31 NC_001527 human 32 NC_001586 human 33 NC_001528 human 34 NC_001587 human 35 NC_001529 human 36 NC_001686 human 37 NC_001687 human 38 NC_001688 human 39 NC_001535 human 40 NC_001589 human 41 NC_001354 human 42 NC_001534 human 44 NC_001689 human 45 NC_001590 human 47 NC_001530 human 48 NC_001690 human 49 NC_001591 human 50 NC_001691 human 51 NC_001533 human 52 NC_001592 human 53 NC_001593 human 54 NC_001676 human 55 NC_001692 human 56 NC_001594 human 57 NC_001353 human 57 b HPU37537 human 58 NC_001443 human 59 NC_001635 human 60 NC_001693 human 61 NC_001694 human 63 NC_001458 human 65 NC_001459 human 66 NC_001695 human 67 D21208 human 68 M73258 human 69 NC_002171 human 70 NC_001711 human 71 NC_002644 human 72 X94164 partial E6;7;1;2;4;L2;1 human 73 X94165 partial E6;7;1;2;4;L2;1 human 74 NC_004501 human 82 NC_002172 human 83 NC_000856 human 84 NC_002676 human 85 AF131950 human 86 NC_003115 human 87 NC_002627 human 89 NC_004103 human 90 NC_004104 human 91 NC_004085 human 92 NC_004500 Accession Organism Type number bovine BPV NC_001522 bovine BPV2 NC_001521 bovine BPV3 NC_004197 bovine BPV4 X05817 D00146 X59063 bovine BPV5 NC_004195 canine Canine oral papillomavirus NC_001619 chimpanzee Common chimpanzee NC_001838 papillomavirus rabbit Cottontail rabbit papillomavirus NC_001541 Deer Deer papillomavirus NC_001523 Equinus Equinus papillomavirus NC_004194 Equus Equus caballus papillomavirus NC_003748 type 1 elk European elk papillomavirus NC_001524 Felis Felis domesticus papillomavirus AF480454 type 1 coelebs Fringilla coelebs papillomavirus NC_004068 Hamster Hamster papovavirus NC_001663 Monkey Monkey B-lymphotropic NC_001536 papovavirus rat Multimammate rat papillomavirus NC_001605 Ovine Ovine papillomavirus 2 NC_001790 Ovine Ovine papillomavirus1 NC_001789 Phocoena Phocoena spinipinnis NC_003348 papillomavirus Psittacus Psittacus erithacus papillomavirus NC_003973 Chimpanzee Pygmy Chimpanzee papilloma X62844 S43934 virus type 1 Rabbit Rabbit oral papillomavirus NC_002232 Reindeer Reindeer papillomavirus NC_004196

Sequences of the reference template sequences: <SEQ25; DNA; Human papillomavirus> tggaccgggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgt <SEQ334; DNA; Human papillomavirus> tggaccgggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgttgtatta gaactaacac ctcaaacaga aattgaccta cagtgcaatg agcaattgga cagctcagag gatgaggatg aggatgaagt agaccatttg caggagcggc cacagcaagc tagacaagct aaacaacata cgtgttacct aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t <SEQ26; DNA; Human papillomavirus> ctaatagcacat ggttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgt <SEQ335; DNA; Human papillomavirus> ctaatagcacat ggttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgttgtatta gaactaacac ctcaaacaga aattgaccta cagtgcaatg agcaattgga cagctcagag gatgaggatg aggatgaagt agaccatttg caggagcggc cacagcaagc tagacaagct aaacaacata cgtgttacct aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t <SEQ27; DNA; Human papillomavirus> aaggtgctacagatgtca aagtccgtta actccggagg aaaagcaatt gcattgtgac agaaaaagac gatttcatct aatagcacat ggttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc <SEQ336; DNA; Human papillomavirus> aaggtgctacagatgtca aagtccgtta actccggagg aaaagcaatt gcattgtgac agaaaaagac gatttcatct aatagcacat ggttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgt <SEQ337; DNA; Human papillomavirus> aaggtgctacagatgtca aagtccgtta actccggagg aaaagcaatt gcattgtgac agaaaaagac gatttcatct aatagcacat ggttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgttgtatta gaactaacac ctcaaacaga aattgaccta cagtgcaatg agcaattgga cagctcagag gatgaggatg aggatgaagt agaccatttg caggagcggc cacagcaagc tagacaagct aaacaacata cgtgttacct aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t <SEQ28; DNA; Human papillomavirus> gttggaccgggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgt <SEQ338; DNA; Human papillomavirus> gttggaccg ggtcatgttt ggggtgctgg agacaaacat ctagagaacc tagagaatct acagtataat catgcatggt aaagtaccaa cgctgcaaga cgttgtatta gaactaacac ctcaaacaga aattgaccta cagtgcaatg agcaattgga cagctcagag gatgaggatg aggatgaagt agaccatttg caggagcggc cacagcaagc tagacaagct aaacaacata cgtgttacct aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t <SEQ29; DNA; Human papillomavirus> tcagaggatgaggatg aggatgaagt agaccatttg caggagcggc cacagcaagc tagacaagct aaacaacata cgtgttacct aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t <SEQ1; DNA; Human papillomavirus> ggcagtggaaagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg <SEQ320; DNA; Human papillomavirus> ggcagtggaaagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact <SEQ321; DNA; Human papillomavirus> ggcagtggaaagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact gtgaaggtac agaggatgag gg <SEQ2; DNA; Human papillomavirus> agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact <SEQ322; DNA; Human papillomavirus> agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg <SEQ323; DNA; Human papillomavirus> agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact gtgaaggtac agaggatgag gg <SEQ3; DNA; Human papillomavirus> atatgcgtgacca gctaccagaa agacgggctg gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gaca <SEQ324; DNA; Human papillomavirus> atatgcgtgacca gctaccagaa agacgggctg gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg <SEQ325; DNA; Human papillomavirus> atatgcgtgacca gctaccagaa agacgggctg gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact <SEQ326; DNA; Human papillomavirus> atatgcgtgacca gctaccagaa agacgggctg gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact gtgaaggtac agaggatgag gg <SEQ327; DNA; Human papillomavirus> atatgcgtgacca gctaccagaa agacgggctg gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcga <SEQ4; DNA; Human papillomavirus> gacaggctacgtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact gtgaaggtac agaggatgag gg <SEQ328; DNA; Human papillomavirus> gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg <SEQ329; DNA; Human papillomavirus> gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact <SEQ330; DNA; Human papillomavirus> gacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcga <SEQ5; DNA; Human papillomavirus> cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcga <SEQ331; DNA; Human papillomavirus> cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg <SEQ332; DNA; Human papillomavirus> cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact <SEQ333; DNA; Human papillomavirus> cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag gtgttcaagt gtagtacaac tggcagtgga aagcagtgga gacacccttc gcgttgtaca gcagatgtta atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact gtgaaggtac agaggatgag gg <SEQ122; DNA; Human papillomavirus> ggacgtggtccaga ttaagtttgc acgaggacga ggacaaggaa aacgatggag actctttgcc aacgtttaaa tgtgtgtcag gaca <SEQ123; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ124; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ125; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ126; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ127; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ128; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ129; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ130; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ131; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ132; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ133; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ134; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ135; DNA; Human papillomavirus> tagtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ136; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ137; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ138; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ139; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ140; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ141; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ142; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ143; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ144; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ145; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ146; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ147; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ359; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ360; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ361; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ362; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ363; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ364; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ365; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ366; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ367; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atctttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ144; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ368; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ369; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ370; DNA; Human papillomavirus> acacccatagt acatttbaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ371; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ372; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ373; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ374; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ375; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ376; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ377; DNA; Human papillomavirus> t agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ378; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ379; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ380; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ381; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ382; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ383; DNA; Human papillomavirus> agtaacacta cacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ384; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ385; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggca cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ386; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca aattaaaata ccaaaaacta ttacagtgtc tactgga <SEQ387; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtggaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ388; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactagatt <SEQ389; DNA; Human papillomavirus> actacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ390; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ391; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ392; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtggaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ393; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ394; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ395; DNA; Human papillomavirus> tacacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ396; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ397; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ398; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ399; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ400; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ401; DNA; Human papillomavirus> acacccatagt acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ148; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ149; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ150; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ151; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ152; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ153; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ154; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgacca <SEQ155; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat tt <SEQ156; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat <SEQ402; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ403; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ404; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ405; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ406; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ407; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ408; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ409; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ410; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat t <SEQ411; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttt <SEQ412; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg <SEQ413; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtc <SEQ163; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ162; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ164; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ414; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ415; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ161; DNA; Human papillomavirus> acatttaaaa ggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ167; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ166; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ168; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ416; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ417; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ165; DNA; Human papillomavirus> ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ159; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ158; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ160; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ418; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ419; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ157; DNA; Human papillomavirus> taaaaggtgatgcta atactttaaa atgtttaaga tatagattta aaaagcattg tacattgtat actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ169; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ170; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ171; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ172; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ173; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ174; DNA; Human papillomavirus> gtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ175; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ176; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ177; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ178; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ179; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ180; DNA; Human papillomavirus> actgcagtgt cgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ181; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ182; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ183; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ184; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ185; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ186; DNA; Human papillomavirus> tgcagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ187; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ188; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ189; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ190; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ191; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ192; DNA; Human papillomavirus> agtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ193; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ194; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ195; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ196; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ197; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ198; DNA; Human papillomavirus> cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ199; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ200; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ201; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ202; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ203; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ204; DNA; Human papillomavirus> tgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ205; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggat <SEQ206; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t <SEQ207; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc <SEQ208; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggattt <SEQ209; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactggatt <SEQ210; DNA; Human papillomavirus> gtgtcgtctacatg gcattggaca ggacataatg taaaacataa aagtgcaatt gttacactta catatgatag tgaatggcaa cgtgaccaat ttttgtctca agttaaaata ccaaaaacta ttacagtgtc tactgga <SEQ46; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ47; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ48; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ49; DNA; Human papillomavirus> gaacaggaatatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ50; DNA; Human papillomavirus> gaacaggaatatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ51; DNA; Human papillomavirus> gaacaggaatatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ52; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg ca <SEQ53; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt <SEQ339; DNA; Human papillomavirus> gaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg ca <SEQ340; DNA; Human papillomavirus> gaacaggaatatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt <SEQ341; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ342; DNA; Human papillomavirus> gaacaggaatatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ54; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg ca <SEQ55; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt <SEQ56; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg ca <SEQ57; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt <SEQ343; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct acagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ344; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ345; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ346; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ347; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ348; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ349; DNA; Human papillomavirus> tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ350; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ345; DNA; Human papillomavirus> ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ351; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ352; DNA; Human papillomavirus> gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca cacctgagtg gatacaaaga cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ58; DNA; Human papillomavirus> tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ59; DNA; Human papillomavirus> tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ60; DNA; Human papillomavirus> gatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ61; DNA; Human papillomavirus> gatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ62; DNA; Human papillomavirus> ggaatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc <SEQ63; DNA; Human papillomavirus> ggaatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ353; DNA; Human papillomavirus> ggaatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ354; DNA; Human papillomavirus> ggaatagatgat agcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ355; DNA; Human papillomavirus> tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ356; DNA; Human papillomavirus> tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ59; DNA; Human papillomavirus> tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc agc <SEQ357; DNA; Human papillomavirus> gatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatg <SEQ358; DNA; Human papillomavirus> gatagcaattttg atttgtcaga aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata tgccttatta gcagacagca acagcaatgc ag <SEQ64; DNA; Human papillomavirus> ggctgatccagaagg tacagacggg gagggcacgg gttgtaacgg ctggttttat gtacaagcta ttgtagacaa aaaaacagga gatgtaatat cagatgacga ggacgaaaat gc <SEQ65; DNA; Human papillomavirus> ggctgatccagaagg tacagacggg gagggcacgg gttgtaacgg ctggttttat gtacaagcta ttgtagacaa aaaaacagga gatgtaatat cagatgacga ggacgaaaat gcaacagaca cagg <SEQ66; DNA; Human papillomavirus> gatccagaagg tacagacggg gagggcacgg gttgtaacgg ctggttttat gtacaagcta ttgtagacaa aaaaacagga gatgtaatat cagatgacga ggacgaaaat gc <SEQ67; DNA; Human papillomavirus> gatccagaagg tacagacggg gagggcacgg gttgtaacgg ctggttttat gtacaagcta ttgtagacaa aaaaacagga gatgtaatat cagatgacga ggacgaaaat gcaacagaca cagg 

We claim:
 1. A process for detecting in a sample at least one HPV, which can be oncogenic for the mucosal epithelia, which comprises contacting said sample or nucleic acid material thereof with HPV amplification primers to amplify at least one HPV nucleic acid from said sample or nucleic acid material by means of said HPV amplification primers and detecting the HPV amplicon(s) thereby produced, if any, wherein the production of at least one HPV amplicon indicates that at least one HPV, which can be oncogenic for the mucosal epithelia, is present in said sample, wherein said HPV amplification primers comprise i/ primers of 14-30 nucleotides, which are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein one primer of a primer pair anneals to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneals to the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide, wherein said at least one template polynucleotide is selected from the group consisting of the HPV18 fragments, which comprise one of the sequences of SEQ ID NOs: 46-51 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence; and ii/ primers of 14-30 nucleotides, which are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein one primer of a primer pair anneals to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneals to the 5′ terminal end of the sequence that is complementary to said at least one template polynucleotide, wherein said at least one template polynucleotide is selected from the group consisting of the HPV16 fragments, which comprise one of the sequences of SEQ ID NOs: 177-180, 189-192 and 195-198 or the complementary sequence thereof or a fragment of said SEQ ID sequence or complementary sequence, wherein said HPV16 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence; wherein said primers of i. are suitable for nucleic acid amplification from one or several HPV selected from the group consisting of HPV18, HPV45, HPV39, HPV59 and HPV68; and wherein said primers of ii. are suitable for nucleic acid amplification from one or several HPV selected from the group consisting of HPV16, HPV31, HPV33, HPV35, HPV52 and HPV58.
 2. The process of claim 1, wherein the primers of i. are suitable for nucleic acid amplification from at least HPV18 and HPV45.
 3. The process of claim 1, wherein the primers of i. are suitable for nucleic acid amplification from HPV18, HPV45, HPV39, HPV59 and HPV68.
 4. The process of claim 1, wherein the primers of ii. are suitable for nucleic acid amplification from at least HPV16, HPV31 and HPV33.
 5. The process of claim 1, wherein the primers of ii. are suitable for nucleic acid amplification from HPV16, HPV31, HPV33, HPV35, HPV52 and HPV58.
 6. The process of claim 1, wherein the primers of i. are suitable for use as primer pairs in the amplification of several of said template polynucleotides.
 7. The process of claim 1, wherein the at least one template polynucleotide of the primers of ii. is selected from the group consisting of the polynucleotides of SEQ ID NOs: 169-210 and the complementary sequences thereof.
 8. The process of claim 1, wherein the primers of ii. are suitable for use as primer pairs in the amplification of several of said template polynucleotides.
 9. The process of claim 1, wherein a primer of the primer pair of i., or of at least one of the primer pairs of i., is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one template polynucleotide, and the other primer of the same primer pair is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide.
 10. The process of claim 1, wherein a primer of the primer pair of i., or of at least one of the primer pairs of i., is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 68-70, and the other primer of the same primer pair is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 79-81.
 11. The process of claim 1, wherein a primer of the primer pair of ii., or of at least one of the primer pairs of ii., is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one template polynucleotide, and the other primer of the same primer pair is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide.
 12. The process of claim 1, wherein a primer of the primer pair of ii., or of at least one of the primer pairs of ii., is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 231-239, and the other primer of the same primer pair is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 256-265.
 13. The process of claim 1, wherein a primer of the primer pair of ii., or of at least one of the primer pairs of ii., is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 232, 234 and 235, and the other primer of the same primer pair is selected from the group consisting of the oligonucleotides of SEQ ID NOs: 258, 261, 264 and
 265. 14. The process of claim 1, wherein the primers of i. and the primers of ii. are in the same amplification container.
 15. The process of claim 1, wherein said detecting comprises contacting said amplicon or at least one of said amplicon(s) with at least one HPV-specific probe in real-time amplification.
 16. The process of claim 1, wherein said detecting comprises contacting said amplicon or at least one of said amplicon(s) with at least one HPV-specific probe, and wherein the oligonucleotide sequence of said at least one HPV-specific probe is at least one of SEQ ID NOs: 88-92 and 277-282, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said at least one HPV-specific probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.
 17. The process of claim 1, wherein said detecting comprises contacting said amplicon or at least one of said amplicon(s) with at least one HPV-specific probe, and wherein said at least one HPV-specific probe consists of at least one of SEQ ID NOs: 102-106 and 304-319, or of one of the complementary sequences thereof, said at least one HPV-specific probe being optionally linked to at least one detection label.
 18. The process of claim 1, wherein said HPV amplification primers further comprise primers of 14-30 nucleotides, which are suitable for use as primer pair(s) in the amplification of at least one HPV selected from the group consisting of the oncogenic HPV belonging to HPV phylogenic groups A5 and A6.
 19. The process of claim 1, wherein said HPV amplification primers further comprise primers of 14-30 nucleotides, which are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein one primer of a primer pair anneals to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneals to the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide, wherein said at least one template polynucleotide is selected from the group consisting of the HPV51 fragments, which comprise the sequence of SEQ ID NO: 5 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV51 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence.
 20. The process of claim 1, wherein said HPV amplification primers further comprise primers of 14-30 nucleotides, which are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein one primer of a primer pair anneals to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneals to the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide, wherein said at least one template polynucleotide is selected from the group consisting of the HPV56 fragments, which comprise the sequence of SEQ ID NO: 25 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV56 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence.
 21. A process of production of HPV primers, which comprises producing at least two oligonucleotides, the respective sequences of which consist of 14-30 nucleotides each and are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein said at least one template polynucleotide is at least one of the HPV18 fragments, which comprise one of the sequences of SEQ ID NOs: 46-51 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence, wherein one primer of a primer pair anneal to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneal to the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide, and wherein said primer pair(s) anneals(anneal) to at least two HPV selected from the group consisting of HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67.
 22. A process of production of HPV primers, which comprises producing at least two oligonucleotides, the respective sequences of which consist of 14-30 nucleotides each and are suitable for use as primer pair(s) in the amplification of at least one template polynucleotide, wherein said at least one template polynucleotide is at least one the HPV16 fragments, which comprise one of the sequences of SEQ ID NOs: 177-180, 189-192 and 195-198 or the complementary sequence thereof or a fragment of said SEQ ID sequence or complementary sequence, wherein said HPV16 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence, wherein one primer of a primer pair anneal to the 5′ terminal end of said at least one template polynucleotide and the other primer of the same primer pair anneal to the 5′ terminal end of the polynucleotide that is complementary to said at least one template polynucleotide, and wherein said primer pair(s) anneals(anneal) to at least two HPV selected from the group consisting of HPV18, HPV45, HPV39, HPV59 and HPV68. 